Protocol

Data Mining in Proteomics

Volume 696 of the series Methods in Molecular Biology pp 123-145

Date:

Tranche Distributed Repository and ProteomeCommons.org

  • Bryan E. SmithAffiliated withDepartments of Biological Chemistry, Bioinformatics and Chemistry, University of Michigan Email author 
  • , James A. HillAffiliated withDepartments of Biological Chemistry, Bioinformatics and Chemistry, University of Michigan
  • , Mark A. GjukichAffiliated withDepartments of Biological Chemistry, Bioinformatics and Chemistry, University of Michigan
  • , Philip C. AndrewsAffiliated withDepartments of Biological Chemistry, Bioinformatics and Chemistry, University of Michigan

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Abstract

Tranche is a distributed repository designed to redundantly store and disseminate data sets for the proteomics community. It has several important features for researchers, including support for large data files, prepublication access controls, licensing options, and ensuring both data provenance and integrity. Tranche tightly integrates with ProteomeCommons.org, an online community resource that offers a variety of useful tools for proteomics researchers, including project management and data annotation. In this chapter, we discuss the development of Tranche and ProteomeCommons.org, paying particular attention to why it is desirable that data be publicly available and unrestricted as well as the challenges facing data archiving and open access. We then provide a technical overview of Tranche and ProteomeCommons.org as well as step-by-step instructions for using these resources, including the graphical user interface (GUI ), command-line tools, and Application Programmer Interface (API). We end with a brief discussion of current and future development efforts and collaborations.