Cold Spring Harbor Laboratory Course on Proteomics

描述(由申请者提供)：建议的冷泉港蛋白质组学实验室课程将于2012年7月7日至22日以及类似的2013年、2014年、2015年和2016年举行。蛋白质组学是系统生物学的支柱技术之一，可以同时对成百上千种蛋白质进行监测和表征。与基因组学和代谢组学方法相结合，蛋白质组学是一项能够并行探索生物活动的核心技术，为哺乳动物发育和疾病的各种生物学过程提供了前所未有的分析能力。许多人类疾病的模型已经在各种各样的动物系统中开发出来，特别是脊椎动物模型，如小鼠、斑马鱼、老鼠和青蛙，以及无脊椎动物模型，如蠕虫和苍蝇；越来越多地利用新的干细胞技术来制造强大的体外模型，以便与动物模型一起部署。对这些模型实施系统生物学方法的需求越来越大，这就需要深入了解各种“高通量”技术的挑战和陷阱，这在一定程度上是通过实践和高度集中的培训实现的。这门密集的实验室和讲座课程将集中在前沿蛋白质组学方法和技术上。学生将获得使用最新技术提纯和识别蛋白质复合体以及翻译后修饰的实践经验。在本课程的蛋白质图谱部分，学生将获得几种定量蛋白质组分析方法的实践经验，包括二维凝胶电泳法和同位素标记策略。学生将接受培训，使用DGE或差示凝胶内电泳法进行基于凝胶的蛋白质定量。差异化表达 蛋白质将使用先进的凝胶分析软件进行统计测定，并使用MALDI质谱仪进行鉴定。对于鸟枪式蛋白质组学分析，学生将学习无标记和共价同位素标记方法，以区分蛋白质组的图谱变化。学生将接受高灵敏度微毛细管液相色谱、纳米喷雾电喷雾离子发射光谱和串联质谱仪的培训。本课程将教授与质谱学相结合的一维和多维分离方法。在课程的目标蛋白质组学部分，将教授学生分析和处理鸟枪式蛋白质组学数据，以开发SRM/MRM分析，以准确识别和量化选定的蛋白质。学生将接受培训以选择和设计目标多肽的转换 并建立和执行SRM/MRM质谱分析。他们将学会处理和解释所获得的数据，以测量和验证各种生物样本中不断变化的目标蛋白质的数量。对于本课程的所有部分，将重点放在数据分析上。外部讲师将讨论本课程未直接涉及的蛋白质组学主题和方法，包括蛋白质阵列、质谱学成像、从头开始的序列分析、自上而下的蛋白质组学、先进的质谱学方法和功能蛋白质组学。本课程的总体目标是为每个学生提供进行和分析蛋白质组学实验所必需的基础知识和实践经验。长期目标是训练学生在他们的生物学研究中识别蛋白质组学方法的新机会和应用，并学习如何将这些方法整合到系统生物学和人类生物学和健康的模型生物体方法中。

DESCRIPTION (provided by applicant): The proposed Cold Spring Harbor Laboratory Course on Proteomics is to be held July 7 - 22, 2012 and similar dates in 2013, 2014, 2015, and 2016. Proteomics is one of the pillar technologies of systems biology by which hundreds or thousands of proteins can be monitored and characterized simultaneously. In combination with genomics and metabolomics approaches, proteomics is an enabling core technology to probe biological activities in parallel, providing unprecedented analytical power into diverse biological processes in mammalian development and disease. Models of many human diseases have been developed in a wide variety of animal systems, in particular vertebrate models such as mouse, zebrafish, rat and frog, and invertebrate models such as worms and flies; and increasingly the use of new stem cell technologies is being harnessed to produce powerful in vitro models to be deployed alongside animal models. There is a growing need for implementation of systems biology approaches to these models, which necessitates an in-depth understanding of the challenges and pitfalls of various "high-throughput" technologies, achieved in part by hands-on and highly focused training. This intensive laboratory and lecture course will focus on cutting-edge proteomics approaches and technologies. Students will gain practical experience purifying and identifying protein complexes and posttranslational modifications using the latest technologies. In the protein profiling portion of the course, students will gain hands-on experience in several quantitative proteome analysis methods, including two-dimensional gel electrophoresis and isotopic labeling strategies. Students will be trained to use DIGE, or differential in-gel electrophoresis, for gel-based protein quantification. Differentially expressed proteins will be statistically determined using advanced gel analysis software, and identified using MALDI mass spectrometry. For shotgun proteomics analysis, students will be taught label-free and covalent isotopic-labeling approaches to differentially profile changes in proteomes. Students will be trained in high-sensitivity microcapillary liquid chromatography coupled with nanospray-ESI and tandem mass spectrometry. Both single dimension and multidimensional separation methods coupled to mass spectrometry will be taught. In the targeted proteomics section of the course, students will be taught to analyze and process shotgun proteomics data to develop SRM/MRM assays to accurately identify and quantify selected proteins. Students will be trained to select and design transitions for targeted peptides and to setup and perform SRM/MRM mass spectrometry assays. They will learn to process and interpret the acquired data to measure and validate changing quantities of targeted proteins in a variety of biological samples. For all sections of the course, a strong emphasis will be placed on data analysis. Outside lecturers will discuss proteomics topics and methods not directly covered in the course including protein arrays, imaging by mass spectrometry, de novo sequence analysis, top-down proteomics, advanced mass spectrometry methods, and functional proteomics. The overall aim of the course is to provide each student with the fundamental knowledge and hands-on experience necessary to be able to perform and analyze proteomics experiments. The long term goal is to train students to identify new opportunities and applications for proteomics approaches in their biological research and to learn how to integrate these into systems biology and model organism approaches to human biology and health.