Unravelling the mysteries of the human proteome: From tools to workflows and analyses
Overview
Seven Bridges is hosting a Proteomics Virtual Workshop along with our collaborators from the NCI Proteomic Data Commons (PDC), on April 21st, from 1 pm to 3 pm EDT. In this workshop, participants will learn how to use the FragPipe proteomics pipeline, developed by members of the Nesvizhskii Lab at the University of Michigan for CPTAC data processing. In addition, participants will learn how to interact with the CGC platform and launch tools on the cloud. This shotgun proteomics pipeline itself consists of the software tools MSFragger, Philosopher, and TMT-integrator, and others.
The FragPipe Proteomics Pipeline, highlighting MSFragger, Philosopher, and TMT-integrator.
What to expect in this workshop
This workshop will feature a hands-on demonstration of navigating the PDC website, linking publicly-available PDC data to personal projects on the CGC, without the need to download or upload, finding files in the CGC Public Apps Gallery, running the shotgun proteomics pipeline, and finally viewing the results. Specifically, this pipeline is designed to process high-throughput data-dependent acquisition (DDA) tandem mass spectrometry data acquired from peptides labeled with TMT tags. The multiplexed labeling, as applied in the CPTAC program, allows for differential quantitation across multiple tumor/normal samples.
Who is the target audience?
We encourage all within the proteomics research community to attend. For this workshop, some basic familiarity with running proteomics processing pipelines is assumed. There is no need to be an expert, but familiarity with proteomics data processing, running pipelines, and Docker will be beneficial.
What is needed to attend?
The main focus of the workshop will be how to run pipelines on the CGC, thus an active CGC account is required. To create an account on the CGC and learn about available pilot funds, click here.
The Team
Dave Roberson
Community Engagement Specialist, Seven Bridges
Felipe da Veiga Leprevost, PhD
Research Investigator, University of Michigan Medical School