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Transformer-DIA

Transformer-based de novo peptide sequencing for data-independent acquisition mass spectrometry

Installation

Dataset

Transformer-DIA usage

Step 0: Data Preparation

  • Split each dataset into train set, validation set, and test set
  • Annotate the spectra file with the corresponding label extracted from feature file
  • Create a new feature file

Step 1: Run de novo sequencing with a pre-trained model:

Step 2: Evaluate de novo sequencing results:

Step 3: Train a new model:

References:

  • Ebrahimi, Shiva, and Xuan Guo. "Transformer-based de novo peptide sequencing for data-independent acquisition mass spectrometry." 2023 IEEE 23rd International Conference on Bioinformatics and Bioengineering (BIBE). IEEE, 2023.