Kusebauch Ulrike, Deutsch Eric W, Campbell David S, Sun Zhi, Farrah Terry, Moritz Robert L
Institute for Systems Biology, Seattle, Washington.
Curr Protoc Bioinformatics. 2014 Jun 17;46:13.25.1-13.25.28. doi: 10.1002/0471250953.bi1325s46.
PeptideAtlas, SRMAtlas, and PASSEL are Web-accessible resources to support discovery and targeted proteomics research. PeptideAtlas is a multi-species compendium of shotgun proteomic data provided by the scientific community; SRMAtlas is a resource of high-quality, complete proteome SRM assays generated in a consistent manner for the targeted identification and quantification of proteins; and PASSEL is a repository that compiles and represents selected reaction monitoring data, all in an easy-to-use interface. The databases are generated from native mass spectrometry data files that are analyzed in a standardized manner including statistical validation of the results. Each resource offers search functionalities and can be queried by user-defined constraints; the query results are provided in tables or are graphically displayed. PeptideAtlas, SRMAtlas, and PASSEL are publicly available freely via the Web site http://www.peptideatlas.org. In this protocol, we describe the use of these resources, we highlight how to submit, search, collate and download data.
PeptideAtlas、SRMAtlas和PASSEL是支持发现和靶向蛋白质组学研究的可通过网络访问的资源。PeptideAtlas是科学界提供的鸟枪法蛋白质组学数据的多物种汇编；SRMAtlas是高质量、完整蛋白质组SRM分析的资源，以一致的方式生成，用于蛋白质的靶向鉴定和定量；PASSEL是一个存储库，它以易于使用的界面汇编并呈现选定的反应监测数据。这些数据库由以标准化方式分析的原始质谱数据文件生成，包括结果的统计验证。每个资源都提供搜索功能，可通过用户定义的约束条件进行查询；查询结果以表格形式提供或以图形方式显示。PeptideAtlas、SRMAtlas和PASSEL可通过网站http://www.peptideatlas.org免费公开获取。在本方案中，我们描述了这些资源的使用方法，重点介绍了如何提交、搜索、整理和下载数据。
