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Improved Peptide Identification for Proteomic Analysis Based on Comprehensive Characterization of Electron Transfer Dissociation Spectra

文献类型：期刊论文

作者Sun, Rui-Xiang1; Dong, Meng-Qiu2; Song, Chun-Qing2; Chi, Hao1; Yang, Bing2; Xiu, Li-Yun1; Tao, Li2; Jing, Ziu-Yi2; Liu, Chao1; Wang, Le-Heng1
刊名JOURNAL OF PROTEOME RESEARCH
出版日期2010-12-01
卷号9期号:12页码:6354-6367
关键词ETD hydrogen rearrangement peptide sequencing search engine
ISSN号1535-3893
DOI10.1021/pr100648r
英文摘要In recent years, electron transfer dissociation (ETD) has enjoyed widespread applications from sequencing of peptides with or without post-translational modifications to top-down analysis of intact proteins However peptide identification rates from ETD spectra compare poorly with those from collision induced dissociation (CID) spectra especially for doubly charged precursors This is in part due to an insufficient understanding of the characteristics of ETD and consequently a failure of database search engines to make use of the rich information contained in the ETD spectra In this study, we statistically characterized ETD fragmentation patterns from a collection of 461 440 spectra and subsequently implemented our findings into pFind a database search engine developed earlier for CID data From ETD spectra of doubly charged precursors pFind 2 1 identified 63-122% more unique peptides than Mascot 2 2 under the same 1% false discovery rate For higher charged peptides as well as phosphopeptides, pFind 2 1 also consistently obtained more identifications Of the features built into pFind 2 1, the following two greatly enhanced its performance (1) refined automatic detection and removal of high-intensity peaks belonging to the precursor charge-reduced precursor or related neutral loss species whose presence often set spectral matching askew, (2) a thorough consideration of hydrogen-rearranged fragment ions such as z + H and c - H for peptide precursors of different charge states Our study has revealed that different charge states of precursors result in different hydrogen rearrangement patterns For a fragment ion, its propensity of gaining or losing a hydrogen depends on (1) the ion type (c or z) and (2) the size of the fragment relative to the precursor and both dependencies are affected by (3) the charge state of the precursor In addition, we discovered ETD characteristics that are unique for certain types of amino acids (AAs), such as a prominent neutral loss of SCH(2)CONH(2) (90 0014 Da) from z ions with a carbamidomethylated cysteine at the N-terminus and a neutral loss of histidine side chain C(4)N(2)H(5) (81 0453 Da) from precursor ions containing histidine The comprehensive list of ETD characteristics summarized in this paper should be valuable for automated database search de novo peptide sequencing and manual spectral validation
资助项目National High Technology Research and Development Program of China[2008AA02Z309] ; National High Technology Research and Development Program of China[2007AA02Z315] ; National High Technology Research and Development Program of China[2007AA02Z1A7] ; National Key Basic Research and Development Program of China[2010CB912701] ; CAS[KGGX1 YW 13] ; National Natural Science Foundation of China[30900262]
WOS研究方向Biochemistry & Molecular Biology
语种英语
WOS记录号WOS:000284856200024
出版者AMER CHEMICAL SOC
源URL[http://119.78.100.204/handle/2XEOYT63/12140]  
专题中国科学院计算技术研究所期刊论文_英文
通讯作者Sun, Rui-Xiang
作者单位1.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China
2.Natl Inst Biol Sci, Beijing 102206, Peoples R China
推荐引用方式
GB/T 7714		 Sun, Rui-Xiang,Dong, Meng-Qiu,Song, Chun-Qing,et al. Improved Peptide Identification for Proteomic Analysis Based on Comprehensive Characterization of Electron Transfer Dissociation Spectra[J]. JOURNAL OF PROTEOME RESEARCH,2010,9(12):6354-6367.
APA Sun, Rui-Xiang.,Dong, Meng-Qiu.,Song, Chun-Qing.,Chi, Hao.,Yang, Bing.,...&He, Si-Min.(2010).Improved Peptide Identification for Proteomic Analysis Based on Comprehensive Characterization of Electron Transfer Dissociation Spectra.JOURNAL OF PROTEOME RESEARCH,9(12),6354-6367.
MLA Sun, Rui-Xiang,et al."Improved Peptide Identification for Proteomic Analysis Based on Comprehensive Characterization of Electron Transfer Dissociation Spectra".JOURNAL OF PROTEOME RESEARCH 9.12(2010):6354-6367.

入库方式： OAI收割

来源：计算技术研究所

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