GENOME DATABASE SEARCHING SOFTWARE FOR ID PROTEINS USING MASS SPECTROMETRY DATA

使用质谱数据搜索 ID 蛋白质的基因组数据库软件

• 批准号: 8169724
• 负责人: ALMA L BURLINGAME
• 金额: $ 12.01万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-12 至 2011-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8169724
• 关键词: Biological Process; Cells; Complex Mixtures; Computer Retrieval of Information on Scientific Projects Database; Computer software; DNA Sequence; Data; Data Set; Databases; Device or Instrument Development; Elements; Enzymes; Funding; Genome; Genomics; Grant; Individual; Institution; Life; Mass Spectrum Analysis; Modification; Molecular Machines; Organism; Peptide Fragments; Peptides; Post-Translational Protein Processing; Protein Array; Protein Databases; Proteins; Reporting; Research; Research Personnel; Resources; Sampling; Software Tools; Source; Techniques; Time; United States National Institutes of Health; design; genome database; helix-loop-helix protein differentiation inhibitor; instrument; mass spectrometer; protein purification; repository; research and development; research study

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The Genome Projects worldwide are rapidly pouring a wealth of DNA sequence data into databases at the National Institutes of Health (NIH) and many other repositories. Within this vast quantity of data lie the largely not-yet-understood blueprints which the individual cells in an organism use to build the array of proteins that serve as the molecular machines for executing the wide variety of biological processes necessary to sustain life. These ever-growing genomic databases serve as a fundamental resource in accelerating research using mass spectrometry for identification of proteins. Mass spectrometry techniques are the most powerful approaches for the characterization of proteins and peptides present in complex mixtures or after protein purification. The most common approach employed for protein identification is to use enzymes to digest proteins into peptides, fragment the peptides in the mass spectrometer and then use database searching software to match the observed peptides to those predicted from sequences in protein databases. However, recent instrument developments now make fragmentation analysis of intact proteins a practical approach. We develop searching software to assist researchers in interpreting both peptide-level and protein-level fragmentation analysis. In addition to identifying proteins, these approaches also have the ability to identify modifications attached to the protein that are used by the cell to regulate protein activity and localization. Experiments can also be designed to compare levels of peptide, modification and protein between related samples to report changes in quantity upon, for example, stimulation. Our software tools are also able to extract these elements of information from datasets. (Additional effort and instrument time reported under Collaborative projects and other Technical Research and Development projects.)

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目和 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 世界各地的基因组计划正在迅速将大量 DNA 序列数据输入美国国立卫生研究院 (NIH) 的数据库和许多其他存储库。 在如此大量的数据中，存在着很大程度上尚未被理解的蓝图，生物体中的各个细胞使用这些蓝图来构建蛋白质阵列，这些蛋白质充当分子机器，用于执行维持生命所需的各种生物过程。这些不断增长的基因组数据库是加速利用质谱鉴定蛋白质的研究的基本资源。 质谱技术是表征复杂混合物中或蛋白质纯化后蛋白质和肽的最有力方法。蛋白质鉴定最常用的方法是使用酶将蛋白质消化成肽，在质谱仪中将肽片段化，然后使用数据库搜索软件将观察到的肽与从蛋白质数据库中的序列预测的肽进行匹配。 然而，最近仪器的发展使得完整蛋白质的碎片分析成为一种实用的方法。 我们开发搜索软件来帮助研究人员解释肽水平和蛋白质水平的碎片分析。 除了识别蛋白质之外，这些方法还能够识别附着在蛋白质上的修饰，细胞利用这些修饰来调节蛋白质活性和定位。 还可以设计实验来比较相关样品之间的肽、修饰和蛋白质的水平，以报告在刺激等情况下的数量变化。 我们的软件工具还能够从数据集中提取这些信息元素。 （在合作项目和其他技术研究与开发项目下报告了额外的工作量和仪器时间。）