TY - JOUR
T1 - Using PeptideAtlas, SRMAtlas, and PASSEL
T2 - Comprehensive resources for discovery and targeted proteomics
AU - Kusebauch, Ulrike
AU - Deutsch, Eric W.
AU - Campbell, David S.
AU - Sun, Zhi
AU - Farrah, Terry
AU - Moritz, Robert L.
PY - 2014/1/1
Y1 - 2014/1/1
N2 - PeptideAtlas, SRMAtlas, and PASSEL areWeb-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 highquality, 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 theWeb 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.
AB - PeptideAtlas, SRMAtlas, and PASSEL areWeb-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 highquality, 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 theWeb 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.
KW - Complete proteome library
KW - Data repository
KW - Data resource
KW - Discovery proteomics
KW - Selected reaction monitoring (SRM)
KW - Targeted proteomics
UR - http://www.scopus.com/inward/record.url?scp=84907958189&partnerID=8YFLogxK
U2 - 10.1002/0471250953.bi1325s46
DO - 10.1002/0471250953.bi1325s46
M3 - Article
C2 - 24939129
AN - SCOPUS:84907958189
SN - 1934-3396
JO - Current Protocols in Bioinformatics
JF - Current Protocols in Bioinformatics
IS - SUPPL.46
M1 - 13.25
ER -