A Frequency-Based Approach to Predict the Low-Energy Collision-Induced Dissociation Fragmentation Spectra

Peptide identification algorithms rely on the comparison between the experimental tandem mass spectrometry spectrum and the theoretical spectrum to identify a peptide from the tandem mass spectra. Hence, it is important to understand the fragmentation process and predict the tandem mass spectra for high-throughput proteomics research. In this study, a novel method was developed to predict the theoretical ion trap collision-induced dissociation (CID) tandem mass spectra of the singly, doubly, and triply charged tryptic peptides. The fragmentation statistics of the ion trap CID spectra were used to predict the theoretical tandem mass spectra of the peptide sequence. The study estimated the relative cleavage frequency for each pair of adjacent amino acids along the peptide length. The study showed that the cleavage frequency can be directly used to predict the tandem mass spectra. The predicted spectra show a high correlation with the experimental spectra used in this study; 99.73% of the high-quality reference spectra have correlation scores greater than 0.8. The new method predicts the theoretical spectrum and correlates significantly better with the experimental spectrum as compared to the existing spectrum prediction tools OpenMS_Simulator, MS2PIP, and MS2PBPI, where only 80, 85.76, and 85.80% of the spectral count, respectively, has a correlation score greater than 0.8.