Seattle Quant: A Resource for the Skyline Software Ecosystem

Development on Skyline started in 2008 to fill a critical need for a software tool to enable targeted proteomics experiments. The development of Skyline grew into an entire ecosystem of tools and has since expanded beyond targeted proteomics. The Skyline software ecosystem is one of the most widely used software platforms in all of mass spectrometry. The current software and its thriving community create exciting new opportunities for quantitative mass spectrometry. As of June 2020, Skyline has been installed >110,000 times, has over 14,000 registered users on its website (http://skyline.ms) and is booted up >9,000 times per week (exceeding 17,500 bootups in a single vveek). The Skyline project has grown beyond the bounds of a single tool. There are now 16 Skyline external tools that rely on a formalized framework in Skyline, with more in development. Some of these tools have been installed >10,000 times. We have also created the Panorama Knowledgebase (http://panoramavveb.org) and Panorama Public, a platform where Skyline users can organize, share, and disseminate processed quantitative proteomics data. Furthermore, our lab is now the primary contributor to Chorus (http://chorusproject.org), a unique mass spectrometry file sharing resource. In this grant, we propose creating a resource that will enable the continued development and maintenance of these community tools and their dissemination within the community. These tools support >14,000 registered users in their basic science, pre-clinical, and translational research. Specifically, our proposal has four aims. 1) Expand our test infrastructure to improve the robustness, stress test the software, confirm compatibility across computer systems, and track performance over time. 2) Improve support for both proteomics and nonproteomics workflows. 3) Improve the collection, sharing, annotation and dissemination of mass spectrometry data and Skyline documents. 4) Provide continued support and training for the Skyline ecosystem.