DICP OpenIR
A Multiplex Fragment-Ion-Based Method for Accurate Proteome Quantification
Liu, Jianhui1,2; Zhou, Yuan1,3; Shan, Yichu1; Zhao, Baofeng1; Hu, Yechen1,2; Sui, Zhigang1; Liang, Zhen1; Zhang, Lihua1; Zhang, Yukui1
Corresponding AuthorZhang, Lihua(lihuazhang@dicp.ac.cn)
Source PublicationANALYTICAL CHEMISTRY
2019-03-19
ISSN0003-2700
DOI10.1021/acs.analchem.8b04806
Volume91Issue:6Pages:3921-3928
Funding ProjectNational Key Research and Development Program of China[2017YFA0505003] ; National Key Research and Development Program of China[2016YFA0501401] ; National Natural Science Foundation[21725506] ; National Natural Science Foundation[91543201] ; National Natural Science Foundation[91753110] ; National Natural Science Foundation[21405154] ; CAS Key Project in Frontier Science[QYZDY-SSW-SLH017] ; Innovation program from DICP, CAS[DICP TMSR201601] ; Innovation program from DICP, CAS[DMTO201701]
Funding OrganizationNational Key Research and Development Program of China ; National Key Research and Development Program of China ; National Natural Science Foundation ; National Natural Science Foundation ; CAS Key Project in Frontier Science ; CAS Key Project in Frontier Science ; Innovation program from DICP, CAS ; Innovation program from DICP, CAS ; National Key Research and Development Program of China ; National Key Research and Development Program of China ; National Natural Science Foundation ; National Natural Science Foundation ; CAS Key Project in Frontier Science ; CAS Key Project in Frontier Science ; Innovation program from DICP, CAS ; Innovation program from DICP, CAS ; National Key Research and Development Program of China ; National Key Research and Development Program of China ; National Natural Science Foundation ; National Natural Science Foundation ; CAS Key Project in Frontier Science ; CAS Key Project in Frontier Science ; Innovation program from DICP, CAS ; Innovation program from DICP, CAS ; National Key Research and Development Program of China ; National Key Research and Development Program of China ; National Natural Science Foundation ; National Natural Science Foundation ; CAS Key Project in Frontier Science ; CAS Key Project in Frontier Science ; Innovation program from DICP, CAS ; Innovation program from DICP, CAS
WOS SubjectChemistry, Analytical
WOS Research AreaChemistry
WOS KeywordTANDEM MASS TAGS ; COMPUTATIONAL PLATFORM ; CANCER ; SPECTROMETRY ; EXPRESSION ; PROTEINS ; STRATEGY ; EMT
AbstractMultiplex proteome quantification with high accuracy is urgently required to achieve a comprehensive understanding of dynamic cellular and physiological processes. Among the existing quantification strategies, fragment-ion based methods can provide highly accurate results, but the multiplex capacity is limited to 3-plex. Herein, we developed a multiplex pseudo-isobaric dimethyl labeling (m-pIDL) method to extend the capacity of the fragment-ion-based method to 6-plex by one-step dimethyl labeling with several millidalton and dalton mass differences between precursor ions and enlarging the isolation window of precursor ions to 10 m/z during data acquisition. m-pIDL showed high quantification accuracy within the 20-fold dynamic range. Notably, the ratio compression was 1.13-fold in a benchmark two-proteome model (5:1 mixed E. coli proteins with HeLa proteins as interference), indicating that by m-pIDL, the ratio distortion of isobaric labeling approaches and the approximate 40% ratio shift of the label free quantification strategy could be effectively eliminated. Additionally, m-pIDL did not show ratio variation among post translational modifications (CV = 6.66%), which could benefit the measurement of universal protein properties for proteomic atlases. We further employed m-pIDL to monitor the time-resolved responses of the TGF-beta-induced epithelial-mesenchymal transition (EMT) in lung adenocarcinoma A549 cell lines, which facilitated the finding of new potential regulatory proteins. Therefore, the 6-plex quantification of m-pIDL with the remarkably high accuracy might create new prospects for comprehensive proteome analysis.
Language英语
Funding OrganizationNational Key Research and Development Program of China ; National Key Research and Development Program of China ; National Natural Science Foundation ; National Natural Science Foundation ; CAS Key Project in Frontier Science ; CAS Key Project in Frontier Science ; Innovation program from DICP, CAS ; Innovation program from DICP, CAS ; National Key Research and Development Program of China ; National Key Research and Development Program of China ; National Natural Science Foundation ; National Natural Science Foundation ; CAS Key Project in Frontier Science ; CAS Key Project in Frontier Science ; Innovation program from DICP, CAS ; Innovation program from DICP, CAS ; National Key Research and Development Program of China ; National Key Research and Development Program of China ; National Natural Science Foundation ; National Natural Science Foundation ; CAS Key Project in Frontier Science ; CAS Key Project in Frontier Science ; Innovation program from DICP, CAS ; Innovation program from DICP, CAS ; National Key Research and Development Program of China ; National Key Research and Development Program of China ; National Natural Science Foundation ; National Natural Science Foundation ; CAS Key Project in Frontier Science ; CAS Key Project in Frontier Science ; Innovation program from DICP, CAS ; Innovation program from DICP, CAS
WOS IDWOS:000462098300023
PublisherAMER CHEMICAL SOC
Citation statistics
Document Type期刊论文
Identifierhttp://cas-ir.dicp.ac.cn/handle/321008/165707
Collection中国科学院大连化学物理研究所
Corresponding AuthorZhang, Lihua
Affiliation1.Chinese Acad Sci, Dalian Inst Chem Phys, CAS Key Lab Separat Sci Analyt Chem, Dalian 116023, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
3.Xuzhou Med Univ, Sch Med Technol, Xuzhou 221004, Jiangsu, Peoples R China
Recommended Citation
GB/T 7714
Liu, Jianhui,Zhou, Yuan,Shan, Yichu,et al. A Multiplex Fragment-Ion-Based Method for Accurate Proteome Quantification[J]. ANALYTICAL CHEMISTRY,2019,91(6):3921-3928.
APA Liu, Jianhui.,Zhou, Yuan.,Shan, Yichu.,Zhao, Baofeng.,Hu, Yechen.,...&Zhang, Yukui.(2019).A Multiplex Fragment-Ion-Based Method for Accurate Proteome Quantification.ANALYTICAL CHEMISTRY,91(6),3921-3928.
MLA Liu, Jianhui,et al."A Multiplex Fragment-Ion-Based Method for Accurate Proteome Quantification".ANALYTICAL CHEMISTRY 91.6(2019):3921-3928.
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