→ Slides, doi: 10.7490/f1000research.1112908.1
This hands-on workshop will take participants through the essential steps for using Galaxy for the analysis of mass spectrometry (MS)-based proteomics data, focusing protein identification from large-scale datasets, and more advanced applications integrating genomic data with proteomic data. Introductory material will be presented on the basics of MS-based proteomics informatics and also emerging applications integrating genomic and proteomic data (an area called proteogenomics).
The workshop will be constructed to follow the steps of proteomic and proteogenomic workflows. Analysis modules corresponding to each of these steps will be described and demonstrated, following the structure below:
Database generation and raw data processing
Attendees will be guided through the use of tools for selecting and generating databases – either standard databases or customized database for proteogenomics derived from genomic data (e.g. RNA-seq data). Tools for converting raw data to processed peak lists for further analysis will also be described.
Sequence database searching
Attendees will learn about 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.
Results visualization and interpretation
Attendees will be exposed to a variety of tools for visualizing and filtering results in Galaxy. Emphasis will be on tools useful for filtering identified proteins from proteogenomic analyses, where quality control of results is essential to generate high confidence results.
At the end of the workshop, attendees will have working knowledge of MS-based proteomics tools in the Tool Shed, experience in setting up basic workflows for protein identification, as well as more advanced applications in proteogenomics. Attendees will also have a better comprehension of the pitfalls encountered when interpreting data from these applications, and tools in Galaxy to help ensure confidence in results.
Participants will be given temporary accounts to a cloud-based Galaxy instance to participate in hands-on workshop activities.