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的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者的研究机构。 全世界的基因组计划正在迅速地将大量的DNA序列数据输入到美国国立卫生研究院（NIH）和许多其他知识库的数据库中。 在这些大量的数据中，存在着大部分尚未被理解的蓝图，生物体中的单个细胞使用这些蓝图来构建蛋白质阵列，这些蛋白质阵列作为执行维持生命所必需的各种生物过程的分子机器。这些不断增长的基因组数据库是加速使用质谱法鉴定蛋白质的研究的基本资源。 质谱（MS）技术在几分钟内从单个样品中产生两种类型的信息。第一个是肽质量值。所谓的肽质量指纹是在使用酶将目标蛋白质消化成称为肽的较小片段的混合物后获得的。用质谱仪测量混合物中每种肽的分子量。由此产生的质量集构成指纹。二是肽序列。在串联MS实验中，未分离或分离的混合物中的单个肽组分可以选择性解离以产生产物离子的光谱（碰撞诱导解离光谱）。所有这些产物离子的质量值的后续测量提供了相邻产物离子之间的质量差，其可以被分配给氨基酸侧链并因此被分配给肽序列。由于这些类型的实验产生的数据的复杂性和MS仪器自动化带来的巨大的样品通量潜力，我们正在继续开发用于从这些CID光谱自动肽序列分配的软件。 在特定蛋白质序列不在这些数据库中的情况下，可以通过手动解释这些CID谱来推断从头序列，这些CID谱可以用于启动基因克隆工作。 或者，可以采用从现有数据库条目检测远程同源性的策略。这些也正在开发中。 （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。）

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 is ever-growing genomic databases serve as a fundamental resource in accelerating research using mass spectrometry for identification of proteins. Mass spectrometry (MS) techniques produce two types of information from a single sample in a matter of minutes. The first are peptide mass values. A so-called peptide-mass fingerprint is obtained after using an enzyme to digest a target protein into a mixture of smaller pieces called peptides. The molecular masses of each peptide in the mixture are measured with a mass spectrometer. The resulting set of masses constitutes a fingerprint. The second is peptide sequence. In a tandem MS experiment individual peptide components in either an unseparated or separated mixture can be selectively dissociated to yield a spectrum of product ions(collision induced dissociation spectrum). Subsequent measurement of the mass values of all of these product ions provides the mass differences between adjacent product ions that can be assigned to amino acid side chain and thus peptide sequence. Because of the complexity of the data produced from these types of experiments and the tremendous sample throughput potential from automation of MS instruments we are continuing to develop software for automatic peptide sequence assignment from these CID spectra. In those situations when the particular protein sequence is not in these databases, de novo sequence can be deduced by manual interpretation of these CID spectra that can be used to initiate gene-cloning efforts. Alternatively, strategies to detect remote homologies from existing database entries can be employed. These are being developed as well. (Additional effort and instrument time reported under Collaborative projects and other Technical Research and Development projects.)