Open AccessUsing PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics
Author(s) -
Kusebauch Ulrike,
Deutsch Eric W.,
Campbell David S.,
Sun Zhi,
Farrah Terry,
Moritz Robert L.
Publication year - 2014
Publication title -
current protocols in bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.535
H-Index - 57
eISSN - 1934-340X
pISSN - 1934-3396
DOI - 10.1002/0471250953.bi1325s46
Subject(s) - compendium , computer science , shotgun proteomics , identification (biology) , resource (disambiguation) , proteomics , data science , world wide web , information retrieval , database , geography , biology , computer network , biochemistry , botany , archaeology , gene
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.