Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics.

Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Curr Protoc Bioinformatics. 2014;46:13.25.1-13.25.28 Authors: Kusebauch U, Deutsch EW, Campbell DS, Sun Z, Farrah T, Moritz RL Abstract 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. Curr. Protoc. Bioinform. 46:13.25.1-13.25.28. © 2014 by John Wiley & Sons, Inc. PMID: 24939129 [PubMed - in process]
Source: Current Protocols in Bioinformatics - Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research