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PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors

文献类型：期刊论文

作者Tarn, Ching1,2; Wu, Yu-Zhuo1,2; Wang, Kai-Fei1,2
刊名JOURNAL OF PROTEOME RESEARCH
出版日期2023-12-29
卷号23期号:2页码:574-584
关键词mass spectrometry peptide identification precursor ion detection deisotope linear programming
ISSN号1535-3893
DOI10.1021/acs.jproteome.3c00293
英文摘要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.
资助项目Natural Science Foundation of China[32071435]
WOS研究方向Biochemistry & Molecular Biology
语种英语
WOS记录号WOS:001157578000001
出版者AMER CHEMICAL SOC
源URL[http://119.78.100.204/handle/2XEOYT63/38369]  
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.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
2.Chinese Acad Sci, Inst Comp Technol, Beijing 100190, 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.

入库方式： OAI收割

来源：计算技术研究所

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