Skyline Targeted Proteomics Environment

Skyline 靶向蛋白质组学环境

• 批准号: 8729603
• 负责人: Michael MacCoss
• 金额: $ 38.63万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-14 至 2016-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8729603
• 关键词: Algorithms; Animal Model; Architecture; Basic Science; Biological; Biological Assay; Biological Markers; Biology; Calibration; Cells; Client; Clinical; Communities; Community Developments; Complex; Complex Mixtures; Computer software; Computers; Data; Data Analyses; Data Collection; Databases; Development; Disease; Engineering; Environment; Failure; Floods; Future; Generations; Genomics; Goals; Grant; Health; Human; Intervention; Laboratories; Letters; Libraries; Liquid Chromatography; Liquid substance; Maintenance; Mass Spectrum Analysis; Measurement; Metadata; Methodology; Methods; Modeling; Monitor; Peptides; Protein Analysis; Proteins; Proteomics; Quality Control; Reaction; Research; Research Personnel; Resolution; Running; Sampling; Scanning; Schedule; Software Tools; Structure; Techniques; Technology; Time; Tissues; Translational Research; Universities; Update; Washington; Writing; assay development; base; candidate validation; case control; data structure; graphical user interface; improved; instrument; interest; mass spectrometer; novel; pre-clinical; repository; research study; tool

DESCRIPTION (provided by applicant): With the maturation of proteomics technologies, these tools are being used to improve our understanding of many basic and clinical questions in human and model organism biology - with the ultimate goal of an improved workflow for biomarker candidate validation. To handle this, laboratories have shown that targeted mass spectrometry measurements offer a promising alternative to immunological based assays. Critical to these experiments is software to handle the generation of instrument methods and the consequent analysis of the resulting data. We have developed a client software tool to handle these analyses called Skyline. In the last 2-3 years, Skyline has become one of the most widely software tools in proteomics. In this grant, we propose to continue the development and maintenance of Skyline, which currently supports hundreds of investigators in their basic science, pre-clinical, and translational research. Specifically, our proposal has five aims. 1) Add support for complex experiment models within Skyline's data structure and graphical user interface. 2) Support calibration curves, complex isotopomer deconvolution, routine statistical analyses within Skyline, and new algorithmic developments by the community within the Skyline architecture. 3) Support the analysis of full scan MS1 and MS/MS data. 4) Support targeted proteomics libraries and implement a repository to store and disseminate targeted proteomics methods. 5) Support automatic method optimization and real-time automatic acquisition parameter updates on ThermoFisher triple quadrupole mass spectrometers.

描述（由申请人提供）：随着蛋白质组学技术的成熟，这些工具被用来提高我们对人类和模型生物学中许多基本和临床问题的理解 - 最终的目标是改善生物标志物候选验证的工作流程。为了解决此问题，实验室表明，有针对性的质谱测量为基于免疫学测定提供了有希望的替代方法。这些实验至关重要的是处理仪器方法生成以及随之而来的数据分析的软件。我们已经开发了一种客户软件工具来处理这些称为Skyline的分析。在过去的2 - 3年中，天际线已成为蛋白质组学中最广泛的软件工具之一。在这笔赠款中，我们建议继续对天际线的开发和维护，目前支持数百名基础科学，临床前和转化研究的研究者。具体来说，我们的建议有五个目标。 1）在Skyline的数据结构和图形用户界面中添加对复杂实验模型的支持。 2）支持校准曲线，复杂的同位素反卷积，天际线内的常规统计分析以及天际线体系结构中社区的新算法发展。 3）支持完整扫描MS1和MS/MS数据的分析。 4）支持有针对性的蛋白质组学库，并实施存储库来存储和传播目标蛋白质组学方法。 5）支持自动方法优化和实时自动采集参数更新三倍四极杆质谱仪。