A universal database reduction method based on the sequence tag strategy to facilitate large-scale database search in proteomics

doi:10.1016/j.ijms.2022.116966

	A universal database reduction method based on the sequence tag strategy to facilitate large-scale database search in proteomics
	Wang, Kai-Fei 1,2; Wu, Yu-Zhuo 1,2; Chi, Hao 1,2
	2023
发表期刊	INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
ISSN	1387-3806
卷号	483 页码:11
摘要	Mass spectrometry-based metaproteomic and proteogenomic studies tend to use large-scale databases that may contain too many irrelevant or artificially constructed proteins. Such an imprecise database presents challenges for both the quality of peptide identification and the time consumption. To address them, we developed a database reduction method for iterative database searching, DBReducer, which can precisely and effectively reduce the large-scale database and is allowed to interface with any down-stream database search engine. In addition, an entrapment strategy was introduced to evaluate the identification precision and recall of different search modes. Compared with the common one-step database search and the traditional iterative database search, the iterative search with DBReducer respectively improved the peptide identification recall from an average of 67.8% and 83.7%-93.5%, and respectively improved the peptide identification precision from an average of 91.1% and 89.6%-91.3%, and more importantly, using DBReducer respectively reduced the time consumption by an average of 57.7% and 68.2%. Our results indicate that DBReducer has the potential to be a widely used database reduction method prior to common proteomic analysis, especially for scenarios with large-scale databases.(c) 2022 Published by Elsevier B.V.
DOI	10.1016/j.ijms.2022.116966
收录类别	SCI
语种	英语
资助项目	Natural Science Foundation of China ; National Key Research and Development Program of China ; [32022046] ; [2016YFA0501301]
WOS研究方向	Physics ; Spectroscopy
WOS类目	Physics, Atomic, Molecular & Chemical ; Spectroscopy
WOS记录号	WOS:000892237100005
出版者	ELSEVIER
引用统计	被引频次：2[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/20246
专题	中国科学院计算技术研究所期刊论文
通讯作者	Chi, Hao
作者单位	1.Chinese Acad Sci, CAS, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Wang, Kai-Fei,Wu, Yu-Zhuo,Chi, Hao. A universal database reduction method based on the sequence tag strategy to facilitate large-scale database search in proteomics[J]. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY,2023,483:11.
APA	Wang, Kai-Fei,Wu, Yu-Zhuo,&Chi, Hao.(2023).A universal database reduction method based on the sequence tag strategy to facilitate large-scale database search in proteomics.INTERNATIONAL JOURNAL OF MASS SPECTROMETRY,483,11.
MLA	Wang, Kai-Fei,et al."A universal database reduction method based on the sequence tag strategy to facilitate large-scale database search in proteomics".INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 483(2023):11.