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PeptideShaker and SearchGUI in Galaxy

Together, SearchGUI and PeptideShaker form a free, cross platform, open source pipeline for peptide and protein identification including some downstream analysis. This page describes efforts by the Galaxy proteomics community to bring the power of these two applications to Galaxy.

The benefits of using SearchGUI and PeptideShaker from within Galaxy include;

  • A client-server model in which multiple users control analyses through a web browser but actual computation is performed by a server application. This is great for tutorials and workshops where users may not have appropriately powerful machines and also for demanding applications, especially those with large mass spec datasets.

  • The ability to create workflows that integrate with some of the many tools available in Galaxy

  • The ability to download a zip file of results from Galaxy that can then be loaded into PeptideShaker for offline inspection.

Tutorials

PeptideShaker and Galaxy are at GCC 2015. Click the links below for course materials

A slightly older tutorial on using PeptideShaker in Galaxy is available here