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学科主题: 物理化学
题名: Interpreting raw biological mass spectra using isotopic mass-to-charge ratio and envelope fingerprinting
作者: Li, Li1, 2;  Tian, Zhixin1, 2
通讯作者: 田志新
刊名: RAPID COMMUNICATIONS IN MASS SPECTROMETRY
发表日期: 2013-06-15
DOI: 10.1002/rcm.6565
卷: 27, 期:11, 页:1267-1277
收录类别: SCI
文章类型: Article
部门归属: DNL20
项目归属: DNL2003
产权排名: 1,1
WOS标题词: Science & Technology ;  Life Sciences & Biomedicine ;  Physical Sciences ;  Technology
类目[WOS]: Biochemical Research Methods ;  Chemistry, Analytical ;  Spectroscopy
研究领域[WOS]: Biochemistry & Molecular Biology ;  Chemistry ;  Spectroscopy
英文摘要: RATIONALE Soft ionization, high-resolution mass spectrometry is widely used to characterize large biological molecules, such as proteins. Deconvolution ('deisotoping') of isotopic envelopes (iEs) in biological mass spectra into monoisotopic or average masses is challenging due to low signals and heavily overlapped iEs, resulting in many wrong interpretations. METHODS Isotopic envelopes (iEs) are directly used without deisotoping to identify biological molecules. An algorithm, isotopic mass-to-charge ratio (m/z) and envelope fingerprinting (iMEF), was implemented in the ProteinGoggle search engine for top-down intact protein database searching. iMEF combines isotopic m/z fingerprinting (iMF) and isotopic envelop fingerprinting (iEF), where 'Isotopic mass-to-charge ratio' means the m/z value of the most abundant isotopic peak within the iE of a precursor or product ion. iMF is used to 'fish' precursor or product ion candidates from the database, which is pre-built and contains all iE information (precursor and product ions) of all proteoforms of the studied system. iEF identifies matching precursor or product ions. A protein is finally identified with user-specified total number of matching product ions and post-translational modification scores. RESULTS The working principles of iMEF and ProteinGoggle, and the definition of a set of related parameters and scoring metrics, are illustrated with high-resolution tandem mass spectrometric analysis of a mixture of ubiquitin and the HUMAN histone H4 proteoforms. Ubiquitin was confidently identified from its CID, ETD, and HCD spectra with 57, 91, and 66 matching product ions, respectively; 125 proteoforms were confidently found from the H4 dataset. The locations of PTMs in 54 and 6 isoforms were partially and fully identified. CONCLUSIONS Database search with iMEF bypasses 'deisotoping' avoiding associated errors, and also provides full quality control of matching precursor and product ions and finally protein IDs. Overlapped iEs of different product ions could also be confidently unwrapped in situ. Improvement and addition of more functionalities and utilities of ProteinGoggle are underway. Copyright (c) 2013 John Wiley & Sons, Ltd.
关键词[WOS]: DECONVOLUTION ;  ALGORITHM ;  SPECTROMETRY ;  ALIGNMENT
语种: 英语
WOS记录号: WOS:000318626500011
Citation statistics: 
内容类型: 期刊论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/117529
Appears in Collections:中国科学院大连化学物理研究所_期刊论文

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作者单位: 1.Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Dalian Natl Lab Clean Energy, Liaoning 116023, Peoples R China
2.Chinese Acad Sci, Dalian Inst Chem Phys, Dalian Natl Lab Clean Energy, Liaoning 116023, Peoples R China

Recommended Citation:
Li, Li,Tian, Zhixin. Interpreting raw biological mass spectra using isotopic mass-to-charge ratio and envelope fingerprinting[J]. RAPID COMMUNICATIONS IN MASS SPECTROMETRY,2013,27(11):1267-1277.
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