A Framework of De Novo Peptide Sequencing for Multiple Tandem Mass Spectra

With tandem mass spectrometry (MS/MS), spectra can be generated by various fragmentation techniques including collision-induced dissociation (CID), higher-energy collisional dissociation (HCD), electron capture dissociation (ECD), electron transfer dissociation (ETD) and so on. At the same time, de novo sequencing using multiple spectra from the same peptide generated by different fragmentation techniques is becoming popular in proteomics studies. The focus of this study is the use of paired spectra from CID (or HCD) and ECD (or ETD) fragmentation because of the complementarity between them. We present a de novo peptide sequencing framework for multiple tandem mass spectra, and apply it to paired spectra sequencing problem. The performance of the framework on paired spectra is compared to another successful method named pNovo+. The results show that our proposed method outperforms pNovo+ in terms of full length peptide sequencing accuracy on three pairs of experimental datasets, with the accuracy increasing up to 13.6% compared to pNovo+.