De novo peptide sequencing using CID and HCD spectra pairs

peer-reviewed · Proteomics · 2016

peer-reviewed · Proteomics · 2016. Yan Yan et al. In tandem mass spectrometry (MS/MS), there are several different fragmentation techniques possible…
Date 2016-10-01
Type peer-reviewed
Venue Proteomics
Publisher Wiley
Contribution algorithm
DOI 10.1002/pmic.201500251
Citations (OpenAlex) 9
Venue 2-year citedness 2.58

Abstract

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%.

Authors

  1. Yan Yan · University of Saskatchewan, University of Western Ontario
  2. Anthony J. Kusalik · University of Saskatchewan
  3. Fang-Xiang Wu · University of Saskatchewan

Methods and tools

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Cited by (1)

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