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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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 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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Internet Resources
  PeptideAtlas. Links to the start pages of the repositories described in this unit.
  SRMAtlas. Links to the start pages of the repositories described in this unit.
  PASSEL. Links to the start pages of the repositories described in this unit.
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