一种位点注释的蛋白质数据库用于磷酸化肽段的鉴定

doi:10.3724/SP.J.1123.2014.10019

色谱 ›› 2015, Vol. 33 ›› Issue (1): 10-16.DOI: 10.3724/SP.J.1123.2014.10019

一种位点注释的蛋白质数据库用于磷酸化肽段的鉴定

程凯^1,2, 王方军¹, 边阳阳^1,2, 叶明亮¹, 邹汉法¹

1. 中国科学院分离分析化学重点实验室, 中国科学院大连化学物理研究所, 国家色谱研究分析中心, 辽宁大连 116023;
2. 中国科学院大学, 北京 100049

收稿日期:2014-10-24 修回日期:2014-11-18 出版日期:2015-01-08 发布日期:2014-12-26
通讯作者: 邹汉法, 叶明亮
基金资助:
国家自然科学基金委员会创新研究群体科学基金项目(21321064);国家重点基础研究发展计划项目(2013CB911202).

Identifying phosphopeptide by searching a site annotated protein database

CHENG Kai^1,2, WANG Fangjun¹, BIAN Yangyang^1,2, YE Mingliang¹, ZOU Hanfa¹

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;
2. University of Chinese Academy of Science, Beijing 100049, China

Received:2014-10-24 Revised:2014-11-18 Online:2015-01-08 Published:2014-12-26

摘要/Abstract

摘要：

磷酸化修饰的分析一直是蛋白质组学研究的热点之一.在鸟枪法的蛋白质组学研究中,通过在数据库检索中设定磷酸化为可变修饰可以直接鉴定磷酸化修饰的位点.但是翻译后修饰的引入会增加数据检索空间,造成鉴定灵敏度的降低.为了解决这一问题,我们构建了一种位点注释的数据库,这种数据库包含蛋白质的磷酸化位点信息,并开发了一种新的数据库检索策略用于磷酸化肽段的可靠鉴定.用不同类型的数据作为分析对象,通过Mascot检索软件对这种新的数据库检索策略进行了考察,证明了这种方法在保证鉴定结果可靠性的前提下提高了磷酸化肽段鉴定的灵敏度.

关键词: 蛋白质组学, 检索空间, 磷酸化, 位点注释

Abstract:

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.

Key words: phosphorylation, proteomics, search space, site annotation

中图分类号:

O658

程凯, 王方军, 边阳阳, 叶明亮, 邹汉法. 一种位点注释的蛋白质数据库用于磷酸化肽段的鉴定[J]. 色谱, 2015, 33(1): 10-16.

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.

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一种位点注释的蛋白质数据库用于磷酸化肽段的鉴定

Identifying phosphopeptide by searching a site annotated protein database

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