Yan Yan, Kusalik Anthony J, Wu Fang-Xiang
Division, of Biomedical Engineering, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
Proteomics. 2016 Oct;16(20):2615-2624. doi: 10.1002/pmic.201500251. Epub 2016 Aug 24.
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%.
在串联质谱法（MS/MS）中，可以采用几种不同的碎裂技术，包括碰撞诱导解离（CID）、高能碰撞解离（HCD）、电子捕获解离（ECD）和电子转移解离（ETD）。在使用成对光谱进行肽段从头测序时，由于CID（或HCD）光谱与ECD（或ETD）光谱之间具有互补性，因此最常用的方法是针对CID（或HCD）和ECD（或ETD）光谱设计的。人们对CID和HCD光谱对的使用关注较少。在本研究中，针对这些光谱对提出了一种新的肽段从头测序方法。该方法包括一个CID和HCD光谱合并标准以及一个母离子质量校正步骤，同时对我们之前提出的用于合并光谱测序的算法进行了改进。使用三对光谱数据集来研究和比较所提出方法与其他为单光谱（HCD或CID）测序设计的现有方法的性能。实验结果表明，在所提出的方法中使用光谱对可显著提高全长肽段测序的准确性，最高准确率达到81.31%。
