Almost all state-of-the-art de novo peptide sequencing algorithms now use machine learning models to encode fragment peaks and hence identify amino acids in mass spectrometry (MS) spectra. Previous work has highlighted how the inherent MS challenges of noise and missing peptide peaks detrimentally affect the performance of these models. In the present research we extracted and evaluated the encoding modules from 3 state-of-the-art de novo peptide sequencing algorithms. We also propose a convolutional neural network-graph neural network machine learning model for encoding peptide ions in tandem MS spectra. We compared the proposed encoding module to those used in the state-of-the-art de novo peptide sequencing algorithms by assessing their ability to identify b-ions and y-ions in MS spectra. This included a comprehensive evaluation in both real and artificial data across various levels of noise and missing peptide peaks. The proposed model performed best across all data sets using two different metrics (area under the receiver operating characteristic curve (AUC) and average precision). The work also highlighted the effect of including additional features such as intensity rank in these encoding modules as well as issues with using the AUC as a metric. This work is of significance to those designing future de novo peptide identification algorithms as it is the first step toward a new approach.
Keywords: de novo peptide sequencing; machine learning; missing peaks; noise.