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The 2022 Galaxy Community Conference (GCC2022) brings together hundreds of researchers, trainers, tool developers, software engineers, and  computational infrastructure providers, all addressing common challenges in data intensive science using the Galaxy data integration and analysis platform.

  • July 17-23, 2022
  • University of Minnesota, Twin Cities
  • Minneapolis, Minnesota, United States

This annual gathering of the Galaxy community includes training, talks, posters, demos, Birds of a Feather meetups, and many other opportunities for collaboration and networking. GCC2022 will be an in-person meeting with limited support for remote attendees. There is no better event than GCC2022 to share your work and learn form others working in data-intensive science.

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Monday, July 18 • 10:20am - 11:20am
16. Galaxy Pipeline for Quantitative Analysis of Enriched Phosphopeptides

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Arthur Eschenlauer, University of Minnesota
Zoi Sychev, University of Minnesota
James Johnson, University of Minnesota
Justin Drake, University of Minnesota

Incorporating a phosphopeptide enrichment step prior to LC-MS (liquid chromatography - mass spectrometry) enhances the sensitivity of detection for the treatment effect on the abundance of phosphorylated proteins (Cheng et al. 2018). However, the raw data are produced at such scale that quantitative data processing is quite cumbersome, so that very few labs are capable of analyzing phosphoproteome data without collaborations with laboratories specialized in the field or with core facilities at considerable cost.

To alleviate these bottlenecks, we have established Galaxy workflows comprising an existing MaxQuant wrapper and new wrappers for subsequent steps: (1) phosphorylation-site localization, (2) mapping of phosphopeptides to proteins and to known phosphorylation and substrate motifs, and (3) ANOVA. The process of wrapping preexisting scripts occasioned the review and improvement of the sequence-search algorithm's efficiency, substantially reducing the time required to execute the pipeline. An additional Kinome-Set Enrichment Analysis module is in development. This pipeline will be made available for deployment to almost any Galaxy instance allowing users at other institutions to analyze phosphoproteomic datasets.

Cheng, L. C., Li, Z., Graeber, T. G., Graham, N. A., & Drake, J. M. (2018). Phosphopeptide Enrichment Coupled with Label-free Quantitative Mass Spectrometry to Investigate the Phosphoproteome in Prostate Cancer. Journal of Visualized Experiments, (138). https://doi.org/10.3791/57996


Speakers
avatar for Arthur Eschenlauer

Arthur Eschenlauer

Researcher 5, University of Minnesota
https://experts.umn.edu/en/persons/art-eschenlauerhttps://orcid.org/0000-0002-2882-0508Art has a Ph.D. in Biochemistry and twenty years experience in the business community supporting Windows and Linux systems and software. Since his return to academia, Art has created tools and developed... Read More →



Monday July 18, 2022 10:20am - 11:20am CDT
Salon ABCD Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

Attendees (5)