PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors

doi:10.1021/acs.jproteome.3c00293

	PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors
	Tarn, Ching 1,2; Wu, Yu-Zhuo 1,2; Wang, Kai-Fei 1,2
	2023-12-29
发表期刊	JOURNAL OF PROTEOME RESEARCH
ISSN	1535-3893
卷号	23 期号:2 页码:574-584
摘要	Accurate and comprehensive peptide precursor ions are crucial to tandem mass-spectrometry-based peptide identification. An identification engine can derive great advantages from the search space reduction enabled by credible and detailed precursors. Furthermore, by considering multiple precursors per spectrum, both the number of identifications and the spectrum explainability can be substantially improved. Here, we introduce PepPre, which detects precursors by decomposing peaks into multiple isotope clusters using linear programming methods. The detected precursors are scored and ranked, and the high-scoring ones are used for subsequent peptide identification. PepPre is evaluated both on regular and cross-linked peptide data sets and compared with 11 methods. The experimental results show that PepPre achieves a remarkable increase of 203% in PSM and 68% in peptide identifications compared to instrument software for regular peptides and 99% in PSM and 27% in peptide pair identifications for cross-linked peptides, surpassing the performance of all other evaluated methods. In addition to the increased identification numbers, further credibility evaluations evidence the reliability of the identified results. Moreover, by widening the isolation window of data acquisition from 2 to 8 Th, with PepPre, an engine is able to identify at least 64% more PSMs, thereby demonstrating the potential advantages of wide-window data acquisition. PepPre is open-source and available at http://peppre.ctarn.io.
关键词	mass spectrometry peptide identification precursor ion detection deisotope linear programming
DOI	10.1021/acs.jproteome.3c00293
收录类别	SCI
语种	英语
资助项目	Natural Science Foundation of China[32071435]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemical Research Methods
WOS记录号	WOS:001157578000001
出版者	AMER CHEMICAL SOC
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/38370
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Tarn, Ching
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Tarn, Ching,Wu, Yu-Zhuo,Wang, Kai-Fei. PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors[J]. JOURNAL OF PROTEOME RESEARCH,2023,23(2):574-584.
APA	Tarn, Ching,Wu, Yu-Zhuo,&Wang, Kai-Fei.(2023).PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors.JOURNAL OF PROTEOME RESEARCH,23(2),574-584.
MLA	Tarn, Ching,et al."PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors".JOURNAL OF PROTEOME RESEARCH 23.2(2023):574-584.