DICP OpenIR
Subject Area物理化学
Large-Scale Quantification of Single Amino-Acid Variations by a Variation-Associated Database Search Strategy
Song, Chunxia1,2; Wang, Fangjun1; Cheng, Kai1; Wei, Xiaoluan1; Bian, Yangyang1; Wang, Keyun1; Tan, Yexiong3; Wang, Hongyang3; Ye, Mingliang1; Zou, Hanfa1; Ye ML(叶明亮); Zou HF(邹汉法)
KeywordSingle Amino-acid Variations Quantification Proteomics Liver Cancer
Source PublicationJOURNAL OF PROTEOME RESEARCH
2014
ISSN1535-3893
DOI10.1021/pr400544j
Volume13Issue:1Pages:241-248
Indexed BySCI
Cooperation Status
SubtypeArticle
Department18
Funding Project1809
Contribution Rank待补充
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Funding Organization1,1 ; 1,1 ; 1,1 ; 1,1
WOS SubjectBiochemical Research Methods
WOS Research AreaBiochemistry & Molecular Biology
WOS KeywordGENOME-WIDE ASSOCIATION ; HEPATOCELLULAR-CARCINOMA ; PHOSPHOPROTEOME ANALYSIS ; PEPTIDE IDENTIFICATION ; SHOTGUN PROTEOMICS ; CELL-LINES ; SUSCEPTIBILITY ; EXPRESSION ; MUTATIONS ; GROWTH
AbstractGlobal quantification of the single amino-acid variations (SAAVs) is essential to investigate the roles of SAAVs in disease progression. However, few efforts have been made on this issue due to the lack of high throughput approach. Here we presented a strategy by integration of the stable isotope dimethyl labeling with variation-associated database search to globally quantify the SAAVs at the first time. A protein database containing 87 745 amino acid variant sequences and 73 910 UniProtKB/Swiss-Prot canonical protein entries was constructed for database search, and higher energy collisional dissociation combined with collision-induced dissociation fragmentation modes were applied to improve the quantification coverage of SAAVs. Compared with target proteomics in which only a few sites could be quantified, as many as 282 unique SAAVs sites were quantified between hepatocellular carcinoma (HCC) and normal human liver tissues-by our strategy. The variation rates in different samples were evaluated, and some interesting SAAVs with significant increase normalized quantification ratios, such as T1406N in CPS1 and S197R in HTATIP2, were observed to highly associate with HCC progression. Therefore, the newly developed strategy enables the large-scale comparative analysis of variations at the protein level and holds a promising future in the research related to variations.
Language英语
Funding Organization1,1 ; 1,1 ; 1,1 ; 1,1
URL查看原文
WOS IDWOS:000329472700024
Citation statistics
Cited Times:14[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://cas-ir.dicp.ac.cn/handle/321008/119756
Collection中国科学院大连化学物理研究所
Corresponding AuthorYe ML(叶明亮); Zou HF(邹汉法)
Affiliation1.Chinese Acad Sci, Dalian Inst Chem Phys, Natl Chromatog R&A Ctr, CAS Key Lab Separat Sci Analyt Chem, Dalian 116023, Peoples R China
2.SINOPEC Res Inst Petr Proc, Beijing 100083, Peoples R China
3.Second Mil Med Univ, Int Cooperat Lab Signal Transduct, Eastern Hepatobiliary Surg Inst, Shanghai 200438, Peoples R China
Recommended Citation
GB/T 7714
Song, Chunxia,Wang, Fangjun,Cheng, Kai,et al. Large-Scale Quantification of Single Amino-Acid Variations by a Variation-Associated Database Search Strategy[J]. JOURNAL OF PROTEOME RESEARCH,2014,13(1):241-248.
APA Song, Chunxia.,Wang, Fangjun.,Cheng, Kai.,Wei, Xiaoluan.,Bian, Yangyang.,...&邹汉法.(2014).Large-Scale Quantification of Single Amino-Acid Variations by a Variation-Associated Database Search Strategy.JOURNAL OF PROTEOME RESEARCH,13(1),241-248.
MLA Song, Chunxia,et al."Large-Scale Quantification of Single Amino-Acid Variations by a Variation-Associated Database Search Strategy".JOURNAL OF PROTEOME RESEARCH 13.1(2014):241-248.
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