title: Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics.
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.
authors.affiliation: Institute for Systems Biology, Seattle, Washington.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Kusebauch
authors.affiliation: Institute for Systems Biology, Seattle, Washington.
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.affiliation: Institute for Systems Biology, Seattle, Washington.
authors.forename: David S
authors.initials: DS
authors.lastname: Campbell
authors.affiliation: Institute for Systems Biology, Seattle, Washington.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Sun
authors.affiliation: Institute for Systems Biology, Seattle, Washington.
authors.forename: Terry
authors.initials: T
authors.lastname: Farrah
authors.affiliation: Institute for Systems Biology, Seattle, Washington.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Moritz
mesh_terms: D000595:Amino Acid Sequence; D001271:Atlases as Topic; D016247:Information Storage and Retrieval; D020407:Internet; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D040901:Proteomics; D017386:Sequence Homology, Amino Acid; D053719:Tandem Mass Spectrometry
chemical_list: D010455:Peptides
keywords: complete proteome library; data repository; data resource; discovery proteomics; selected reaction monitoring (SRM); targeted proteomics