NovoHCD: de novo peptide sequencing from HCD spectra

In recent years, de novo peptide sequencing from mass spectrometry data has developed as one of the major peptide identification methods with the emergence of new instruments and advanced computational methods. However, there are still limitations to this method; for example, the typically used spectrum graph model cannot represent all the information and relationships inherent in tandem mass spectra (MS/MS spectra). Here, we present a new method named NovoHCD which applies a spectrum graph model with multiple types of edges (called a multi-edge graph), and integrates into it amino acid combination (AAC) information and peptide tags. In addition, information on immonium ions observed particularly in higher-energy collisional dissociation (HCD) spectra is incorporated. Comparisons between NovoHCD and another successful de novo peptide sequencing method for HCD spectra, pNovo, were performed. Experiments were conducted on five HCD spectral datasets. Results show that NovoHCD outperforms pNovo in terms of full length peptide identification accuracy; specifically, the accuracy increases 13%-21% over the five datasets.