GCC 2017

➔ Tutorial

The Galaxy bioinformatics platform has emerged as a valuable resource for mass spectrometry (MS) based proteomic informatics. An active community of researchers and users, including the Galaxy for proteomics (Galaxy-P) team, continues to extend Galaxy for these applications.

This hands-on workshop will guide participants through the essential steps for using Galaxy for the analysis of MS-based proteomics data, focusing on protein identification and more advanced multi-omic applications. Workflows from emerging applications integrating genomic and proteomic data (such as proteogenomics and metaproteomics) will also be demonstrated.

In order to extend the reach of these workflows to the greater community, the Galaxy-P team has partnered with both the JetStream cyberinfrastructure resource (http://jetstream-cloud.org/) and Amazon Web Services (https://aws.amazon.com).

The workshop will be constructed to follow the steps based on the structure below:

1. Instructions on how to access the resource (30 minutes)
   • This workshop will provide participants background on Galaxy-P software and workflows that have been made available on the resource. Attendees will take away knowledge on how to access this resource and possibly make use of it for their own MS-based proteomics informatics needs.
2. Introduction to Proteomics (1 hour)
   • Attendees will learn about inputs for proteomics search and also available software in Galaxy for sequence database searching, which identifies proteins via matching of MS data to sequence databases. Use of these tools and optimization of parameters will be demonstrated and discussed.
3. Multi-omics Workflows ( 1 hour) Attendees will be exposed to a variety of tools and workflows for filtering results in Galaxy. Emphasis will be on these two workflows
   1. Proteogenomics Workflow: Used for filtering identified peptides from proteogenomic analyses.
   2. Metaproteomics Workflow: Used for identifying genera from identified peptides from metaproteomics analysis.

At the end of the workshop, attendees will have working knowledge of MS-based proteomics tools; experience in setting up basic workflows for protein identification, as well as more advanced workflows in proteogenomics and metaproteomics. 

Participants will be given temporary accounts to a cloud-based Galaxy instance to participate in hands-on workshop activities.

• Galaxy 101 or equivalent experience.
• A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best.