GENOME DATABASE SEARCHING SOFTWARE FOR ID PROTEINS USING MASS SPECTROMETRY DATA

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 世界各地的基因组计划正在迅速将丰富的DNA序列数据注入美国国立卫生研究院(NIH)和许多其他储存库的数据库中。在这海量的数据中，隐藏着在很大程度上还不为人所知的蓝图，生物体中的单个细胞用来构建蛋白质阵列，这些蛋白质充当分子机器，执行维持生命所必需的各种生物过程。这些不断增长的基因组数据库是加速利用质谱学鉴定蛋白质的研究的基本资源。 质谱学技术是鉴定复杂混合物或蛋白质纯化后存在的蛋白质和多肽的最有效的方法。蛋白质鉴定最常用的方法是使用酶将蛋白质消化成多肽，在质谱仪中将这些多肽碎片，然后使用数据库搜索软件将观察到的多肽与蛋白质数据库中的序列预测的多肽进行匹配。然而，最近的仪器发展使完整蛋白质的片段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多肽水平和蛋白质水平的碎片分析。除了识别蛋白质外，这些方法还具有识别附着在蛋白质上的修饰的能力，这些修饰被细胞用来调节蛋白质的活性和定位。还可以设计实验来比较相关样品之间的多肽、修饰和蛋白质的水平，以报告例如刺激时的数量变化。我们的软件工具也能够从数据集中提取这些信息元素。 (在协作项目和其他技术研究和开发项目下报告的额外工作量和仪器时间。)

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.)