Seattle Quant: A Resource for the Skyline Software Ecosystem

Seattle Quant：Skyline 软件生态系统的资源

• 批准号: 10189938
• 负责人: Michael MacCoss
• 金额: $ 111.38万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-05-01 至 2026-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10189938
• 关键词: Area; Basic Science; Biological Assay; Cellular Assay; Clinical Research; Collection; Communities; Computer Systems; Computer software; Data; Data Analyses; Data Scientist; Data Store; Development; Dictionary; Disease; Documentation; Ecosystem; Educational workshop; Ensure; Generations; Genes; Grant; Growth; Health; Immunologics; Infrastructure; Laboratory Research; Maintenance; Mass Spectrum Analysis; Measurement; Metadata; Methods; Molecular; Monitor; Ontology; Peptides; Performance; Phenotype; Process; Production; Protein Analysis; Proteins; Proteomics; Publishing; Quality Control; Reaction; Reading; Research; Research Personnel; Resource Sharing; Resources; Software Tools; Stress Tests; System; Technology; Testing; Time; Training; Translational Research; Vendor; Work; base; biomedical scientist; computerized data processing; data integration; data reuse; experimental study; improved; innovation; instrument; knowledge base; lipidomics; mass spectrometer; meetings; metabolomics; method development; pre-clinical research; small molecule; software development; support tools; synergism; tandem mass spectrometry; tool; web site; webinar

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.

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的开发成长为一个完整的工具生态系统，并在此后不断扩展 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 所有质谱分析的平台。当前的软件及其蓬勃发展的社区创造了令人兴奋的新 定量质谱的机会。截至2020年6月，Skyline已安装超过110，000次， 在其网站（http：//www.example.com）上拥有超过14，000名注册用户，每周启动次数超过9，000次skyline.ms （单周启动次数超过17，500次）。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， 发展其中一些工具已安装超过10，000次。我们也创造了全景 知识库（panoramaweb.org）和全景公共平台，天际线用户可以组织， 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 Chorus（http：//www.example.com）的贡献者，这是一个独特的质谱文件共享资源。chorusproject.org在这 赠款，我们建议创建一个资源，使这些持续发展和维护 社区工具及其在社区内的传播。这些工具支持超过14，000名注册用户 在基础科学、临床前和转化研究方面。具体而言，我们的建议有四个目标。第一章 扩展我们的测试基础设施，以提高健壮性，对软件进行压力测试， 计算机系统，并跟踪性能随着时间的推移。2)提高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)改进质谱的收集、共享、注释和传播 数据和Skyline文档。4)为Skyline生态系统提供持续的支持和培训。