Bidirectional de novo peptide sequencing using a transformer model.

ABSTRACT

In proteomics, a crucial aspect is to identify peptide sequences. De novo sequencing methods have been widely employed to identify peptide sequences, and numerous tools have been proposed over the past two decades. Recently, deep learning approaches have been introduced for de novo sequencing. Previous methods focused on encoding tandem mass spectra and predicting peptide sequences from the first amino acid onwards. However, when predicting peptides using tandem mass spectra, the peptide sequence can be predicted not only from the first amino acid but also from the last amino acid due to the coexistence of b-ion (or a- or c-ion) and y-ion (or x- or z-ion) fragments in the tandem mass spectra. Therefore, it is essential to predict peptide sequences bidirectionally. Our approach, called NovoB, utilizes a Transformer model to predict peptide sequences bidirectionally, starting with both the first and last amino acids. In comparison to Casanovo, our method achieved an improvement of the average peptide-level accuracy rate of approximately 9.8% across all species.