Citation: CHENG Kai, WANG Fangjun, BIAN Yangyang, YE Mingliang, ZOU Hanfa. Identifying phosphopeptide by searching a site annotated protein database[J]. Chinese Journal of Chromatography, ;2015, 33(1): 10-16. doi: 10.3724/SP.J.1123.2014.10019 shu

Identifying phosphopeptide by searching a site annotated protein database

CHENG Kai ^1,2 ,
WANG Fangjun ¹ ,
BIAN Yangyang ^1,2 ,
YE Mingliang ^1,, ,
ZOU Hanfa ^1,,

1.
1. Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, National Chromatographic Research and Analysis Center, Dalian 116023, China;

Corresponding author: YE Mingliang, ZOU Hanfa,
Received Date: 24 October 2014
Available Online: 18 November 2014
Fund Project: 国家自然科学基金委员会创新研究群体科学基金项目(21321064) (21321064)国家重点基础研究发展计划项目(2013CB911202). (2013CB911202)

Phosphoproteome analysis is one of the important research fields in proteomics. In shotgun proteomics, phosphopeptides could be identified directly by setting phosphorylation as variable modifications in database search. However, search space increases significantly when variable modifications are set in post-translation modifications (PTMs) analysis, which will decrease the identification sensitivity. Because setting a variable modification on a specific type of amino acid residue means all of this amino acid residues in the database might be modified, which is not consistent with actual conditions. Phosphorylation and dephosphorylation are regulated by protein kinases and phosphatases, which can only occur on particular substrates. Therefore only residues within specific sequence are potential sites which may be modified. To address this issue, we extracted the characteristic sequence from the identified phosphorylation sites and created an annotated database containing phosphorylation site information, which allowed the searching engine to set variable modifications only on the serine, threonine and tyrosine residues that were identified to be phosphorylated previously. In this database only annotated serine, threonine and tyrosine can be modified. This strategy significantly reduced the search space. The performance of this new database searching strategy was evaluated by searching different types of data with Mascot, and higher sensitivity for phosphopeptide identification was achieved with high reliability.
- proteomics,
- phosphorylation,
- search space,
- site annotation
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沈阳化工大学材料科学与工程学院沈阳 110142

Identifying phosphopeptide by searching a site annotated protein database

南开大学师唯/华北电力大学（保定）刘景维：二维配位聚合物中有序的亲锂冠醚位点用于无枝晶锂沉积

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通讯作者: 陈斌, bchen63@163.com