Seattle Quant: A Resource for the Skyline Software Ecosystem

Skyline的开发始于2008年，以满足对实现靶向蛋白质组学的软件工具的迫切需求 实验。Skyline的开发发展成了一个完整的工具生态系统，并自那以后得到了扩展 超越靶向蛋白质组学。Skyline软件生态系统是使用最广泛的软件之一 在所有的质谱学平台上。当前的软件及其蓬勃发展的社区创造了令人兴奋的新 定量质谱学的机会。截至2020年6月，Skyline已经安装了11万次。 在其网站(http://skyline.ms))上有超过14,000名注册用户，每周启动9000次 (一周内超过17,500次启动)。天际线项目已经超越了单一的 工具。现在有16个Skyline外部工具依赖于Skyline中的正式框架，更多的工具在 发展。其中一些工具已经被安装了一万次。我们还创建了全景图 知识库(http://panoramaweb.org)和全景公共，天际用户可以组织的平台， 共享和传播经过处理的定量蛋白质组学数据。此外，我们的实验室现在是主要的 合唱团(http://chorusproject.org)，)的贡献者，一个独特的质谱学文件共享资源。在这 Grant，我们建议创建一种资源，使这些资源能够继续开发和维护 社区工具及其在社区内的传播。这些工具支持14,000个注册用户 在基础科学、临床前和转化性研究方面。具体地说，我们的建议有四个目标。1) 扩展我们的测试基础架构以提高健壮性、对软件进行压力测试、确认 计算机系统，并随着时间的推移跟踪性能。2)改善对蛋白质组学和非蛋白质组学的支持 蛋白质组学工作流程。3)完善质谱学的收集、共享、注释和传播 数据和天际线文档。4)为天际生态系统提供持续支持和培训。

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 week). 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://panoramaweb.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 non- proteomics 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.