De novo peptide sequencing using CID and HCD spectra pairs.
In tandem mass spectrometry (MS/MS), there are several different fragmentation techniques possible, including, collision-induced dissociation (CID) higher energy collisional dissociation (HCD), electron-capture dissociation (ECD), and electron transfer dissociation (ETD). When using pairs of spectra for de novo peptide sequencing, the most popular methods are designed for CID (or HCD) and ECD (or ETD) spectra because of the complementarity between them. Less attention has been paid to the use of CID and HCD spectra pairs. In this study, a new de novo peptide sequencing method is proposed for these spectra pairs. This method includes a CID and HCD spectra merging criterion and a parent mass correction step, along with improvements to our previously proposed algorithm for sequencing merged spectra. Three pairs of spectral datasets were used to investigate and compare the performance of the proposed method with other existing methods designed for single spectrum (HCD or CID) sequencing. Experimental results showed that full-length peptide sequencing accuracy was increased significantly by using spectra pairs in the proposed method, with the highest accuracy reaching 81.31%.
['Yan|Yan|Y|', 'Kusalik|Anthony J|AJ|', 'Wu|Fang-Xiang|FX|']
D000465:Algorithms D006801:Humans D010455:Peptides D040901:Proteomics D020539:Sequence Analysis, Protein D053719:Tandem Mass Spectrometry
De novo peptide sequencing CID HCD Tandem mass spectrometry Spectra merging Bioinformatics