Loevenich Sandra N, Brunner Erich, King Nichole L, Deutsch Eric W, Stein Stephen E, Aebersold Ruedi, Hafen Ernst
Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
BMC Bioinformatics. 2009 Feb 11;10:59. doi: 10.1186/1471-2105-10-59.
Crucial foundations of any quantitative systems biology experiment are correct genome and proteome annotations. Protein databases compiled from high quality empirical protein identifications that are in turn based on correct gene models increase the correctness, sensitivity, and quantitative accuracy of systems biology genome-scale experiments.
In this manuscript, we present the Drosophila melanogaster PeptideAtlas, a fly proteomics and genomics resource of unsurpassed depth. Based on peptide mass spectrometry data collected in our laboratory the portal http://www.drosophila-peptideatlas.org allows querying fly protein data observed with respect to gene model confirmation and splice site verification as well as for the identification of proteotypic peptides suited for targeted proteomics studies. Additionally, the database provides consensus mass spectra for observed peptides along with qualitative and quantitative information about the number of observations of a particular peptide and the sample(s) in which it was observed.
PeptideAtlas is an open access database for the Drosophila community that has several features and applications that support (1) reduction of the complexity inherently associated with performing targeted proteomic studies, (2) designing and accelerating shotgun proteomics experiments, (3) confirming or questioning gene models, and (4) adjusting gene models such that they are in line with observed Drosophila peptides. While the database consists of proteomic data it is not required that the user is a proteomics expert.
任何定量系统生物学实验的关键基础都是正确的基因组和蛋白质组注释。从高质量的经验性蛋白质鉴定中编译的蛋白质数据库，而这些鉴定又基于正确的基因模型，可提高系统生物学基因组规模实验的正确性、灵敏度和定量准确性。
在本论文中，我们展示了果蝇肽图集（Drosophila melanogaster PeptideAtlas），这是一个深度无与伦比的果蝇蛋白质组学和基因组学资源。基于我们实验室收集的肽质谱数据，门户网站http://www.drosophila-peptideatlas.org允许查询关于基因模型确认和剪接位点验证所观察到的果蝇蛋白质数据，以及用于鉴定适合靶向蛋白质组学研究的蛋白型肽。此外，该数据库提供了所观察到的肽的一致性质谱图，以及关于特定肽的观察次数和观察到该肽的样本的定性和定量信息。
肽图集是一个面向果蝇研究群体的开放获取数据库，具有多种功能和应用，可支持：（1）降低与进行靶向蛋白质组学研究固有相关的复杂性；（2）设计和加速鸟枪法蛋白质组学实验；（3）确认或质疑基因模型；（4）调整基因模型，使其与观察到的果蝇肽相符。虽然该数据库由蛋白质组学数据组成，但并不要求用户是蛋白质组学专家。
