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学科主题: 物理化学
题名: Improve the Coverage for the Analysis of Phosphoproteome of HeLa Cells by a Tandem Digestion Approach
作者: Bian, Yangyang1, 2;  Ye, Mingliang1;  Song, Chunxia1, 2;  Cheng, Kai1, 2;  Wang, Chunli1, 2;  Wei, Xiaoluan1;  Zhu, Jun1, 2;  Chen, Rui1, 2;  Wang, Fangjun1;  Zou, Hanfa1
通讯作者: 叶明亮 ;  邹汉法
关键词: tandem protease digestion ;  Glu-C ;  phosphorylation sites ;  phosphoproteomics ;  LC-MS/MS ;  kinase motif
刊名: JOURNAL OF PROTEOME RESEARCH
发表日期: 2012-05-01
DOI: 10.1021/pr300242w
卷: 11, 期:5, 页:2828-2837
收录类别: SCI
文章类型: Article
部门归属: 18
项目归属: 1809
产权排名: 1,1
WOS标题词: Science & Technology ;  Life Sciences & Biomedicine
类目[WOS]: Biochemical Research Methods
研究领域[WOS]: Biochemistry & Molecular Biology
英文摘要: Complete coverage of all phosphorylation sites in a proteome is the ultimate goal for large-scale phosphoproteome analysis. However, only making use of one protease trypsin for protein digestion cannot cover all phosphorylation sites, because not all tryptic phosphopeptides are detectable in MS. To further increase the phosphoproteomics coverage of HeLa cells, we proposed a tandem digestion approach by using two different proteases. By combining the data set of the first Glu-C digestion and the second trypsin digestion, the tandem digestion approach resulted in the identification of 8062 unique phosphopeptides and 8507 phosphorylation sites in HeLa cells. The conventional trypsin digestion approach resulted in the identification of 3891 unique phosphopeptides and 4647 phosphorylation sites. It was found that the phosphorylation sites identified from the above two approaches were highly complementary. By combining above two data sets, in total we identified 10899 unique phosphopeptides and 11262 phosphorylation sites, corresponding to 3437 unique phosphoproteins with FDR < 1% at peptide level. We also compared the kinase motifs extracted from trypsin, Glu-C, or a second trypsin digestion data sets. It was observed that basophilic motifs were more frequently found in the trypsin and the second trypsin digestion data sets, and the acidic motifs were more frequently found in the Glu-C digestion data set. These results demonstrated that our tandem digestion approach is a good complement to the conventional trypsin digestion approach for improving the phosphoproteomics analysis coverage of HeLa cells.
关键词[WOS]: SCALE PHOSPHORYLATION ANALYSIS ;  MASS-SPECTROMETRY ;  PROTEIN-PHOSPHORYLATION ;  PHOSPHOPEPTIDE ENRICHMENT ;  SACCHAROMYCES-CEREVISIAE ;  CHROMATOGRAPHY ;  SEPARATION ;  ELASTASE ;  STRATEGY ;  SITES
语种: 英语
WOS记录号: WOS:000303492100017
Citation statistics: 
内容类型: 期刊论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/118236
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, Natl Chromatog R&A Ctr, Key Lab Separat Sci Analyt Chem, Dalian 116023, Peoples R China
2.Chinese Acad Sci, Grad Sch, Beijing 100049, Peoples R China

Recommended Citation:
Bian, Yangyang,Ye, Mingliang,Song, Chunxia,et al. Improve the Coverage for the Analysis of Phosphoproteome of HeLa Cells by a Tandem Digestion Approach[J]. JOURNAL OF PROTEOME RESEARCH,2012,11(5):2828-2837.
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