Unit

UNIT 13.25 Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics

  1. Ulrike Kusebauch,
  2. Eric W. Deutsch,
  3. David S. Campbell,
  4. Zhi Sun,
  5. Terry Farrah,
  6. Robert L. Moritz

Published Online: 17 JUN 2014

DOI: 10.1002/0471250953.bi1325s46

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Kusebauch, U., Deutsch, E. W., Campbell, D. S., Sun, Z., Farrah, T. and Moritz, R. L. 2014. Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Current Protocols in Bioinformatics. 46:13.25:13.25.1–13.25.28.

Author Information

  1. Institute for Systems Biology, Seattle, Washington

Publication History

  1. Published Online: 17 JUN 2014

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. Curr. Protoc. Bioinform. 46:13.25.1-13.25.28. © 2014 by John Wiley & Sons, Inc.

Keywords:

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