Software to Identify Post-translational Modifications From Proteomic Data Sets

从蛋白质组数据集中识别翻译后修饰的软件

• 批准号: 7895216
• 负责人: Morgan Corinne GIDDINGS
• 金额: $ 16.96万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-31 至 2011-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7895216
• 关键词: Software; Identify; Post; translational; Modifications

DESCRIPTION (provided by applicant): Proteins are the workhorses of cells, comprising much of the machinery of life. Chemical changes due to co- or post-translational modifications, or amino acid substitutions resulting from genetic variation, can alter protein function and have significant consequences on the functioning of a cell. Pinpointing chemical changes in proteins in an automated manner remains an elusive goal. Mass spectrometry (MS) based methodologies are promising for examining such alterations, since they are exquisitely sensitive to the resulting shifts in mass. There are two main approaches that can be used for examining proteins by MS, one which measures the intact masses of proteins to detect shifts indicative of modifications (called top-down), and the other which enzymatically digests proteins into short peptides, then analyzes their chemical structure by tandem mass spectrometry (called bottom-up). Each of the existing MS methods has limitations, such as lack of complete protein coverage for bottom-up, and the inability to use top-down data to uniquely identify modifications; these drawbacks have motivated the development of hybrid combinations such as "top-down bottom-up" (TDBU) proteomics. Though these are seeing a surge of interest, there is an acute lack of comprehensive, automated software for combining measurements from the distinct MS approaches; thus, studies to date have relied upon extensive manual analysis and/or ad hoc program scripts, inhibiting progress in the field. We propose to address this issue using our two existing programs, PROCLAME for analyzing top-down data, and GFS for analyzing bottom-up data, to develop integrated, open-source software that combines data from multiple MS methodologies to pinpoint posttranslational modifications and amino acid substitutions in proteins. Our aims are: 1) to integrate multiple MS data sources for determining the type and location of modifications on proteins, by adding a Markov chain Monte Carlo (MCMC) based engine to PROCLAME; 2) to improve the ability to analyze bottom-up data by enhancing GFS for the automatic determination of posttranslational modifications; 3) to manage and integrate results from multiple MS measurements and search engines, by developing a database system and scripts to tie the programs together; and 4) to assure program reliability and suitability through both alpha testing in-house and beta testing at external sites. Health Relevance: Both amino acid substitutions and misregulation of enzymes that modify proteins play roles in human diseases such as Cancer, Diabetes, Sickle Cell Anemia, and many others. This proposal is to build generalized software that can be used by a broad base of researchers to pinpoint the chemical changes/modifications to proteins that perturb regulatory networks in cells to cause disease.NARRATIVE Both amino acid substitutions and misregulation of enzymes that modify proteins play roles in human diseases such as Cancer, Diabetes, Sickle Cell Anemia, and many others. This proposal is to build generalized software that can be used by a broad base of researchers to pinpoint the chemical changes and modifications to proteins that perturb regulatory networks in cells to cause disease, by integrating data from the latest proteomic technologies.

描述（由申请人提供）：蛋白质是细胞的工作主场，其中包括生命的大部分机械。由于遗传变异而导致的氨基酸修饰或氨基酸取代引起的化学变化可以改变蛋白质功能，并对细胞的功能产生重大影响。以自动化方式指出蛋白质的化学变化仍然是一个难以捉摸的目标。基于质谱（MS）的方法学有望检查此类改变，因为它们对所得质量变化非常敏感。有两种主要方法可用于通过MS检查蛋白质，一种方法可以测量蛋白质的完整质量，以检测指示修饰的移位（称为自上而下），而另一种则可以将酶消化成短肽中，然后通过临时质谱分析其化学结构（称为底部）。每个现有的MS方法都有局限性，例如缺乏自下而上的完整蛋白质覆盖范围，以及无法使用自上而下的数据来唯一识别修改；这些缺点激发了混合组合的发展，例如“自上而下”（TDBU）蛋白质组学。尽管这些引起了人们的兴趣，但急性缺乏全面的自动化软件来结合不同MS方法的测量。因此，迄今为止的研究依赖于大量的手动分析和/或临时程序脚本，从而抑制了该领域的进展。 我们建议使用我们的两个现有程序来解决此问题，即用于分析自上而下的数据，以及用于分析自下而上数据的GFS，以开发集成的，开源的软件，这些软件将来自多个MS方法的数据结合到蛋白质中的多个MS方法和精确的氨基酸替代。我们的目标是：1）通过将基于马尔可夫链蒙特卡洛（MCMC）的发动机添加到proclame中，整合多个MS数据源来确定蛋白质修饰的类型和位置； 2）通过增强GFS自动确定翻译后修饰的能力来提高分析自下而上的数据的能力； 3）通过开发数据库系统和脚本将程序绑定在一起，来管理和整合来自多个MS测量和搜索引擎的结果； 4）通过内部测试和在外部站点的Alpha测试和Beta测试来确保计划的可靠性和适用性。 健康相关性：氨基酸的取代和酶的不调节，这些酶修饰蛋白质在癌症，糖尿病，镰状细胞性贫血等人类疾病中起着作用。该建议是建立广泛的软件，可以由广泛的研究人员使用，以查明对细胞中扰动调节网络的蛋白质的化学变化/修饰以引起疾病。 氨基酸的取代和修饰蛋白质在癌症，糖尿病，镰状细胞贫血等人类疾病中起作用的酶的不正当。该建议是建立广泛的软件，该软件可以由广泛的研究人员使用，以通过整合来自最新的蛋白质组学技术的数据来查明对细胞扰动细胞的蛋白质的化学变化和修饰，以引起疾病。