DICP OpenIR
Subject Area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)
Source PublicationRAPID COMMUNICATIONS IN MASS SPECTROMETRY
2013-06-15
DOI10.1002/rcm.6565
Volume27Issue:11Pages:1267-1277
Indexed BySCI
SubtypeArticle
DepartmentDNL20
Funding ProjectDNL2003
Contribution Rank1,1
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine ; Physical Sciences ; Technology
WOS SubjectBiochemical Research Methods ; Chemistry, Analytical ; Spectroscopy
WOS Research AreaBiochemistry & Molecular Biology ; Chemistry ; Spectroscopy
WOS KeywordDECONVOLUTION ; ALGORITHM ; SPECTROMETRY ; ALIGNMENT
AbstractRATIONALE 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.
Language英语
WOS IDWOS:000318626500011
Citation statistics
Document Type期刊论文
Identifierhttp://cas-ir.dicp.ac.cn/handle/321008/117529
Collection中国科学院大连化学物理研究所
Corresponding AuthorTian ZX(田志新)
Affiliation1.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
GB/T 7714
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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