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. 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. Our laboratory has developed a client software tool to handle these analyses called Skyline. In the last 8 years, Skyline has become one of the most widely software tools in proteomics and mass spectrometry. In this grant, we propose to continue the development and maintenance of Skyline and its associated software ecosystem, which currently supports 1000s of investigators in their basic science, pre-clinical, and translational research. Specifically, our proposal has five 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 non-proteomics workflows. 3) Improve the collection, sharing, and dissemination of quantitative mass spectrometry data. 4) Modify Skyline to work in a cloud computing environment. 5) Provide continued support and training for the Skyline ecosystem.
Mass spectrometry has been a fundamental technology for the analysis of proteins in health and disease. Targeted mass spectrometry measurements offer a promising alternative to immunological based assays that are the standard for quantitative protein measurements in clinical and basic research laboratories. Critical to these experiments is our software, Skyline and the associated ecosystem of tools, which have been developed to handle the generation of instrument methods and the subsequent analysis of the resulting data.
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