基于ProteinGoggle 2.0的组蛋白H4蛋白质变体的自上而下表征

引用本文: 肖开捷, 田志新. 基于ProteinGoggle 2.0的组蛋白H4蛋白质变体的自上而下表征[J]. 色谱, 2016, 34(12): 1255-1263. doi: 10.3724/SP.J.1123.2016.09012 shu

Citation: XIAO Kaijie, TIAN Zhixin. Top-down characterization of histone H4 proteoforms with ProteinGoggle 2.0[J]. Chinese Journal of Chromatography, 2016, 34(12): 1255-1263. doi: 10.3724/SP.J.1123.2016.09012 shu

基于ProteinGoggle 2.0的组蛋白H4蛋白质变体的自上而下表征

肖开捷 ,
田志新

同济大学化学科学与工程学院, 上海市化学品分析、风险评估与控制重点实验室, 上海 200092
基金项目:
China State Key Basic Research Program (No. 2013CB911203)

National Natural Science Foundation of China (No. 21575104)

Shanghai Science and Technology Commission (No. 14DZ2261100).

摘要: 由于大量可能蛋白质变体以及每一个翻译后修饰大量可能位点的存在，核心组蛋白上密集的组合式翻译后修饰的自上而下表征一直是一个巨大的分析挑战。结合高分辨串级质谱，基于同位素质荷比和轮廓指纹比对的整体蛋白质数据库搜索引擎ProteinGoggle 2.0在组蛋白翻译后修饰的自上而下鉴定方面拥有诸多独特的优势。该文报道ProteinGoggle 2.0对HeLa核心组蛋白H4的数据库搜索及蛋白质变体的鉴定结果。基于从UniProt网站下载的人类核心组蛋白H4的纯文本文件和“鸟枪法”注释，ProteinGoggle 2.0首先创建包含所有可能蛋白质变体的理论数据库；从纯文本文件中提取的信息主要是氨基酸序列、可能的翻译后修饰（单甲基化、二甲基化、三甲基化、乙酰化和磷酸化）及氨基酸变异（A77→P）。在控制质谱水平假阳性率低于1%的前提下，共鉴定到426个蛋白质变体，这是目前为止H4蛋白质变体的最全报道。这些ProteinGoggle 2.0鉴定到的H4蛋白质变体也与之前报道的ProSightPC 2.0的鉴定结果进行了肩并肩比较。总而言之，ProteinGoggle 2.0可以对具有复杂组合修饰及氨基酸变异的蛋白质组进行数据库搜索和蛋白质变体鉴定。

关键词:

English

Top-down characterization of histone H4 proteoforms with ProteinGoggle 2.0

XIAO Kaijie ,
TIAN Zhixin

School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
Received Date: 04 September 2016
Fund Project:
China State Key Basic Research Program (No. 2013CB911203)

National Natural Science Foundation of China (No. 21575104)

Shanghai Science and Technology Commission (No. 14DZ2261100).

Abstract: Top-down characterization of combinatorial and dense post-translational modifications (PTMs) on core histones has long been a big analytical challenge because of enormous putative proteoforms for identification and simultaneously enormous putative sites of each individual PTM for localization. ProteinGoggle 2.0, as implemented with the isotopic mass-to-charge ratio and envelope fingerprinting algorithm, has multiple unique strengths for top-down characterization of histone PTMs together with high-resolution tandem mass spectrometry. Here we report our database search and proteoform identification of HeLa core histone H4 using ProteinGoggle 2.0. The Theoretical database containing all putative proteoforms was created with shotgun annotation from the human H4 flat text downloaded from UniProt; information including the amino acid sequence, putative PTMs (methylation, di-methylation, tri-methylation, acetylation and phosphorylation) and amino acid variation (A77 to P) was adopted from the flat text file. A total of 426 proteoforms were confidently identified with a spectrum level false discovery rate of less than 1%, which represents the most comprehensive H4 proteoforms reported so far. Side-by-side comparison of these proteoforms with those identified by ProSightPC 2.0 was also made. By and large, ProteinGoggle 2.0 can be adopted for database search and proteoform identification of proteins with multiple combinatorial PTMs as well as amino acid variation.

Key words:

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基于ProteinGoggle 2.0的组蛋白H4蛋白质变体的自上而下表征

English

Top-down characterization of histone H4 proteoforms with ProteinGoggle 2.0

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基于ProteinGoggle 2.0的组蛋白H4蛋白质变体的自上而下表征

English

Top-down characterization of histone H4 proteoforms with ProteinGoggle 2.0

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

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CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

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