Development of New Proteomics Technology and its Application to Study Cellular Organization

解读发育中mRNA和蛋白质动力学之间的关系 原始脊椎动物 母奖的广泛目标（新蛋白质组学技术的发展及其 应用于研究细胞组织）是推进定量蛋白质组学技术 并将其应用于获得对细胞组织的系统级理解。最近我们 证明了TMTproC显着提高了灵敏度和多路复用能力的 互补报告离子方法，同时使这些方法与广泛的 质谱仪（约翰逊，2021）。我们还努力改善获得高- 通过将TMTproC与仅离子阱仪器集成，获得高质量的蛋白质组学数据， 少于通常用于多重定量蛋白质组学的那些。我们已经成功 利用我们的蛋白质组学技术开发进行多种合作（Crapse，2021; 哈特，2020年;曹，2020年），这促进了我们对细胞组织的理解。一 该实验室的重点是更好地了解发展进程（阮，2021; Keber，2021; Nofal，2021年）。最近，我们发表了一份预印本，表明在青蛙胚胎中， 蛋白质在发育过程中通过输入亲和力以时间顺序进入细胞核， 从而作为一个优雅的定时机制，以控制其下游的开始， 函数（Nguyen，2021）。除了我们在发育生物学方面的工作， 开发的方法，使我们能够参数化蛋白质丰度控制的所有方面， 通过转录、翻译和降解的多组学整合实现全球规模。关键 这些进展正在开发允许无扰动测量的新方法 蛋白质周转到目前为止，我们已经将这些方法应用于E。大肠杆菌和酵母（Gupta，等，在 准备），亚历克斯·弗雷斯正在将这些方法扩展到正在发育的玻璃海鞘胚胎 目的是将这些技术推广到复杂的高等生物，如非洲爪蟾， 和果蝇。

Deciphering the Relationship Between mRNA and Protein Dynamics in a Developing Proto-Vertebrate The broad goal of the parent award (Development of New Proteomics Technology and its Application to Study Cellular Organization) is to advance quantitative proteomics technology and apply it to obtain a systems level understanding of cellular organization. Recently, we have demonstrated that TMTproC significantly increases sensitivity and multiplexing capacity of the complement reporter ion approach while making these approaches compatible with a broad set of mass spectrometers (Johnson, 2021). We have also worked to improve access to high- quality proteomics data by integrating TMTproC with ion-trap only instruments which cost 80% less than ones typically used for multiplexed quantitative proteomics. We have successfully leveraged our proteomics technology development for multiple collaborations (Crapse, 2021; Hart, 2020; Cao, 2020) which has advanced our understanding of cellular organization. One focus of the lab is to better understand developmental progression (Nguyen, 2021; Keber, 2021; Nofal, 2021). Recently, we have published a preprint showing that, in frog embryos, nuclear proteins access the nucleus in a temporal order set via importin affinities during development, thereby acting as an elegant timing mechanism to control the onset of their downstream functions (Nguyen, 2021). Extending beyond our work in developmental biology, we have developed methods that allow us to parameterize all aspects of protein abundance control on a global scale through multi-omics integration of transcription, translation, and degradation. Key to these advances was developing new methods that allow measurement of perturbation-free protein turnover. So far, we have applied these methods to E. coli and yeast (Gupta, et al., in preparation), and Alex Frese is expanding these approaches to the developing Ciona embryo with the goal of generalizing these techniques to complex higher organisms such as Xenopus and Drosophila.