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

Curr Protoc Bioinformatics. 2014 Jun 17:46:13.25.1-13.25.28. doi: 10.1002/0471250953.bi1325s46.

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.

Keywords: complete proteome library; data repository; data resource; discovery proteomics; selected reaction monitoring (SRM); targeted proteomics.

Publication types

  • Research Support, American Recovery and Reinvestment Act
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Atlases as Topic*
  • Information Storage and Retrieval
  • Internet
  • Molecular Sequence Data
  • Peptides / chemistry*
  • Proteomics*
  • Sequence Homology, Amino Acid
  • Tandem Mass Spectrometry

Substances

  • Peptides