DICP OpenIR
学科主题物理化学
Interpreting raw biological mass spectra using isotopic mass-to-charge ratio and envelope fingerprinting
Li, Li1,2; Tian, Zhixin1,2; Tian ZX(田志新)
刊名RAPID COMMUNICATIONS IN MASS SPECTROMETRY
2013-06-15
DOI10.1002/rcm.6565
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
关键词[WOS]DECONVOLUTION ; ALGORITHM ; SPECTROMETRY ; ALIGNMENT
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.
语种英语
WOS记录号WOS:000318626500011
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被引频次:19[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://cas-ir.dicp.ac.cn/handle/321008/117529
专题中国科学院大连化学物理研究所
通讯作者Tian ZX(田志新)
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
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Li, Li,Tian, Zhixin,Tian ZX. 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.
APA Li, Li,Tian, Zhixin,&田志新.(2013).Interpreting raw biological mass spectra using isotopic mass-to-charge ratio and envelope fingerprinting.RAPID COMMUNICATIONS IN MASS SPECTROMETRY,27(11),1267-1277.
MLA Li, Li,et al."Interpreting raw biological mass spectra using isotopic mass-to-charge ratio and envelope fingerprinting".RAPID COMMUNICATIONS IN MASS SPECTROMETRY 27.11(2013):1267-1277.
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