Reprint of 鈥減Find-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data鈥?

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• 作者：Hao Chi^a ; Kun He^a ; Bing Yang^b ; Zhen Chen^c ; Rui-Xiang Sun^a ; Sheng-Bo Fan^a ; Kun Zhang^a ; Chao Liu^a ; Zuo-Fei Yuan^a ; Quan-Hui Wang^c ; Si-Qi Liu^c ; Meng-Qiu Dong^b ; Si-Min He^a ; ^{smhe@ict.ac.cn" class="auth_mail" title="E-mail the corresponding author}
• 关键词：Unrestricted database search ; Ion index ; In-depth interpretation ; High resolution MS/MS
• 刊名：Journal of Proteomics
• 出版年：2015
• 出版时间：3 November 2015
• 年：2015
• 卷：129
• 期：Complete
• 页码：33-41
• 全文大小：1043 K

文摘

Database search is the dominant approach in high-throughput proteomic analysis. However, the interpretation rate of MS/MS spectra is very low in such a restricted mode, which is mainly due to unexpected modifications and irregular digestion types. In this study, we developed a new algorithm called Alioth, to be integrated into the search engine of pFind, for fast and accurate unrestricted database search on high-resolution MS/MS data. An ion index is constructed for both peptide precursors and fragment ions, by which arbitrary digestions and a single site of any modifications and mutations can be searched efficiently. A new re-ranking algorithm is used to distinguish the correct peptide-spectrum matches from random ones. The algorithm is tested on several HCD datasets and the interpretation rate of MS/MS spectra using Alioth is as high as 60%–80%. Peptides from semi- and non-specific digestions, as well as those with unexpected modifications or mutations, can be effectively identified using Alioth and confidently validated using other search engines. The average processing speed of Alioth is 5–10 times faster than some other unrestricted search engines and is comparable to or even faster than the restricted search algorithms tested.This article is part of a Special Issue entitled: Computational Proteomics.