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

Ulrike Kusebauch1, Eric W. Deutsch1, David S. Campbell1, Zhi Sun1, Terry Farrah1, Robert L. Moritz1

1 Institute for Systems Biology, Seattle, Washington
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 13.25
DOI:  10.1002/0471250953.bi1325s46
Online Posting Date:  June, 2014
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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

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Explore the PeptideAtlas Database
  • Basic Protocol 2: Submit Raw MS Data to PeptideAtlas
  • Basic Protocol 3: SRMAtlas: Query and Download SRM Assays for Direct Deployment in Targeted Proteomic Experiments
  • Basic Protocol 4: PASSEL: Browse, Query and Download Publicly Available SRM Experiments
  • Alternate Protocol 1: Filter and Query SRM Results Across all Experiments in the PASSEL Database
  • Basic Protocol 5: Submit SRM Results to the PASSEL Data Repository
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

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Internet Resources
  http://www.peptideatlas.org/
  PeptideAtlas. Links to the start pages of the repositories described in this unit.
  http://www.srmatlas.org/
  SRMAtlas. Links to the start pages of the repositories described in this unit.
  http://www.peptideatlas.org/passel/
  PASSEL. Links to the start pages of the repositories described in this unit.
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