Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics.
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.
['Kusebauch|Ulrike|U|', 'Deutsch|Eric W|EW|', 'Campbell|David S|DS|', 'Sun|Zhi|Z|', 'Farrah|Terry|T|', 'Moritz|Robert L|RL|']
D000595:Amino Acid Sequence D001271:Atlases as Topic D016247:Information Storage and Retrieval D020407:Internet D008969:Molecular Sequence Data D010455:Peptides D040901:Proteomics D017386:Sequence Homology, Amino Acid D053719:Tandem Mass Spectrometry
targeted proteomics complete proteome library data repository data resource discovery proteomics selected reaction monitoring (SRM)