The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data.
The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data.
复制标题
DOI：
10.1186/1471-2105-8-156
复制
发表时间：
2007-05-16
影响因子：
3
通讯作者：
Griffin PR
中科院分区：
文献类型：
--
作者：
Pascal BD;Chalmers MJ;Busby SA;Mader CC;Southern MR;Tsinoremas NF;Griffin PR
质谱与液相酰胺氢/氘交换（H/D交换）实验的结合是表征蛋白质动力学、蛋白质-蛋白质或蛋白质-配体相互作用的有效方法。尽管仪器和自动化方面取得了方法上的进步和改进，但数据分析和显示仍然是一个乏味的过程。造成这一瓶颈的因素是典型实验中产生的大量数据点，每个数据点都需要手动管理和验证，然后计算主链酰胺交换水平。已经有一些工具可以解决其中一些问题，但缺乏满足 H/D 交换社区需求所需的足够集成、功能和可访问性。迄今为止，还没有用于分析 H/D 交换数据的软件可以全面解决这些问题。我们开发了一个集成软件系统，用于自动分析和表示 H/D 交换数据，其名称为“The Deuterator”。已经实施的新方法能够实现高通量分析、氘掺入的自动测定以及重叠肽的解卷积。这是通过使用涉及迭代理论包络拟合的方法以及考虑预期 m/z 范围内的峰值数据来实现的。利用现有的通用文件格式，可以与无数 MS 仪器平台和肽序列数据库搜索引擎的输出兼容。基于网络的界面用于集成 Deuterator 的组件，这些组件能够分析和呈现来自具有不同分辨率的仪器的质谱数据。如有必要，可以对结果进行确认、调整、重新计算和保存。其他工具将策划的计算参数与复制时间点同步，从而提高吞吐量。然后，保存的结果可用于绘制氘累积曲线和 3D 结构叠加。该系统已经在生产环境中成功使用了一年多，并且可以在项目主页上作为网络工具免费使用。在用户界面中自动计算和呈现 H/D 交换数据使科学家能够有效地组织和分析数据。 Deuterator 不同组件的集成加上通用数据文件格式的灵活性使得该系统可供不断扩大的 H/D 交换社区使用。
The combination of mass spectrometry and solution phase amide hydrogen/deuterium exchange (H/D exchange) experiments is an effective method for characterizing protein dynamics, and protein-protein or protein-ligand interactions. Despite methodological advancements and improvements in instrumentation and automation, data analysis and display remains a tedious process. The factors that contribute to this bottleneck are the large number of data points produced in a typical experiment, each requiring manual curation and validation, and then calculation of the level of backbone amide exchange. Tools have become available that address some of these issues, but lack sufficient integration, functionality, and accessibility required to address the needs of the H/D exchange community. To date there is no software for the analysis of H/D exchange data that comprehensively addresses these issues. We have developed an integrated software system for the automated analysis and representation of H/D exchange data that has been titled "The Deuterator". Novel approaches have been implemented that enable high throughput analysis, automated determination of deuterium incorporation, and deconvolution of overlapping peptides. This has been achieved by using methods involving iterative theoretical envelope fitting, and consideration of peak data within expected m/z ranges. Existing common file formats have been leveraged to allow compatibility with the output from the myriad of MS instrument platforms and peptide sequence database search engines. A web-based interface is used to integrate the components of The Deuterator that are able to analyze and present mass spectral data from instruments with varying resolving powers. The results, if necessary, can then be confirmed, adjusted, re-calculated and saved. Additional tools synchronize the curated calculation parameters with replicate time points, increasing throughput. Saved results can then be used to plot deuterium buildup curves and 3D structural overlays. The system has been used successfully in a production environment for over one year and is freely available as a web tool at the project home page . The automated calculation and presentation of H/D exchange data in a user interface enables scientists to organize and analyze data efficiently. Integration of the different components of The Deuterator coupled with the flexibility of common data file formats allow this system to be accessible to the broadening H/D exchange community.
登录
查看更多内容
影响因子：
7.4
作者：
Chik, JK;Graaf, JLV;Schriemer, DC
通讯作者：
Schriemer, DC
影响因子：
8
作者：
Hotchko, M;Anand, GS;Ten Eyck, LF
通讯作者：
Ten Eyck, LF
DOI：
10.1016/s1044-0305(01)00301-4
发表时间：
2001-11-01
影响因子：
3.2
作者：
Palmblad, M;Buijs, J;Håkansson, P
通讯作者：
Håkansson, P
影响因子：
1.8
作者：
YERGEY, JA
通讯作者：
YERGEY, JA
DOI：
10.1016/j.jasms.2006.06.006
发表时间：
2006-11-01
影响因子：
3.2
作者：
Englander, S. Walter
通讯作者：
Englander, S. Walter