Abstract
With tandem mass spectrometry (MS/MS), spectra can be generated by various methods including collision-induced dissociation (CID), higher-energy collisional dissociation (HCD), electron capture dissociation (ECD) and electron transfer dissociation (ETD). At the same time, de novo sequencing using multiple spectra from the same peptide is becoming popular in proteomics studies. The focus of this work is using a pair of spectra from CID (or HCD) and ECD (or ETD) fragmentation because of the complementarity between them. We present a new de novo sequencing method for such paired spectra named NovoPair, and compare its performance to another successful method named pNovo+. NovoPair extends our previously proposed graph model to suit paired spectra, and considers different ion types in the two spectra to extract more information. The results show that NovoPair 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+.