WORKSHOP AND TRAINING ACTIVITIES

研讨会和培训活动

• 批准号: 8170700
• 负责人: RICHARD D SMITH
• 金额: $ 3.32万
• 依托单位: BATTELLE PACIFIC NORTHWEST LABORATORIES
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-01 至 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8170700
• 关键词: Algorithms; Alzheimer' s Disease; American; Apple; Area; Arts; Awareness; Belgium; Biochemical; Biology; Biomedical Research; Biomedical Technology; Boxing; Brain; Breast Cancer Cell; California; Cell Fractionation; Cell physiology; Cellular biology; Collaborations; Communities; Complex; Computer Retrieval of Information on Scientific Projects Database; Computer software; Data; Data Analyses; Data Set; Diabetes Mellitus; Disease model; District of Columbia; Educational workshop; Environment; Evolution; Experimental Designs; Explosion; Fostering; Foundations; Fractionation; Funding; Future; Genomics; Goals; Grant; HIV Infections; Hepatic; Human; Image; Individual; Informatics; Institutes; Institution; International; Investigation; Islet Cell; Islets of Langerhans; Kidney Transplantation; Korea; Koreans; Laboratories; Length; Link; Liquid Chromatography; Liquid substance; Longevity; Lyme Disease; Malignant neoplasm of prostate; Mass Spectrum Analysis; Measurement; Membrane Microdomains; Metabolism; Methodology; Methods; Modeling; Mus; National Center for Research Resources; Nature; Netherlands; Neurites; North Carolina; Oranges; Oregon; Oxidative Stress; Pattern; Peer Review; Peptides; Phosphoric Monoester Hydrolases; Post-Translational Protein Processing; Progress Reports; Proteins; Proteome; Proteomics; Publications; Regulation; Reporting; Research; Research Personnel; Research Project Grants; Research Training; Resolution; Resources; Rest; Sampling; San Francisco; Science; Scientist; Signal Transduction; Signal Transduction Pathway; Societies; Software Tools; Solid; Solutions; Source; Stable Isotope Labeling; Subgroup; System; Systems Biology; Technology; Texas; Tissues; Training; Training Activity; Trees; Trust; United States National Institutes of Health; Universities; Urine; Visit; Washington; Work; abstracting; base; cancer cell; cell growth; comparative; design; forest; improved; interest; macrophage; meetings; new technology; novel strategies; open source; programs; protein complex; relating to nervous system; research study; response; software development; sound; stem; symposium; tool; tool development; web site

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Accessibility of advanced proteomics technologies to the biomedical community is a longer-term goal of the Research Center. This information transfer is made possible by the NCRR website (full details on website on page 26 of the Research Progress Report) and the hosting of workshops and tutorials. Since the establishment of our NCRR program, the Center has organized two NCRR workshops and participated in six short courses/tutorials. A Short Course titled, "Data Extraction and Analysis for LC-MS Based Proteomics" was given at the U.S. HUPO meeting in San Diego, CA in February 2009. This is the third consecutive year that the PNNL NCRR informatics team has presented this invited course. The course covered several aspects of quantitative proteomics using LC-MS analysis platforms, including an overview of quantitative approaches and software tools available to the community, considerations for experimental design, feature discovery in LC-MS datasets, and statistically sound analysis of identified peptides and proteins. These topics were aimed at informing researchers about the issues to consider when designing LC-MS experiments, while also describing the general approaches used for extracting information content from LC-MS data. The 15 people in attendance each received a data disk (DVD) with the software installers for proteomics software developed at the Center, plus the example data used to prepare the presentation. A Short Course titled, "Data Extraction and Analysis for LC-MS Based Proteomics" was given at the U.S. HUPO meeting in Bethesda, MD in March 2008. The course covered several aspects of quantitative proteomics using LC-MS analysis platforms, including a comparison of the approaches and software tools available to the community, considerations for experiment design, feature discovery in LC-MS datasets, and statistically sound analysis of identified peptides and proteins. These topics were aimed at informing researchers about the issues to consider when designing LC-MS experiments, while also describing the general approaches used for extracting information content from LC-MS data. The ~35 people in attendance received a data disk (DVD) with the software installers for proteomics software developed at PNNL, plus the example data used to prepare the figures shown in the presentation. A Short Course titled, "Data Extraction and Analysis for LC-MS Based Proteomics" was given at the U.S. HUPO meeting in Seattle, WA in March 2007. The course was intended to educate the U.S. proteomics community and discuss the use of two different LC-MS data extraction and analysis platforms to demonstrate how high mass measurement accuracy mass spectrometry and high resolution liquid chromatography could be applied for higher-throughput proteomics. The topics presented include 1) LC-MS feature extraction, 2) experimental design and analysis of large LC-MS datasets, and 3) identification and characterization of peptides and proteins using LC-MS. These topics were aimed at getting increased information content from LC-MS experiments both within customized and commercially available LC-MS systems. A number of informatics tools and algorithms were described, many of which are either open-source or freely available at the NCRR website. A DVD was also distributed to attendees with software installers and demo data. A Special Interest Subgroup titled, "Managing the Data Explosion in Systems Biology" was held at the American Society for Cell Biology (ASCB) Meeting in San Diego, CA in December 2006. The following abstract summarizes the Special Interest Subgroup at the ASCB meeting entitled: New technologies in genomics, proteomics, and quantitative imaging are producing enormous amounts of data that promise to revolutionize biology in the upcoming decades. To realize this potential, however, new approaches must be developed to manipulate, integrate and analyze the large datasets that these technologies can generate. Otherwise, the trees will continue to obscure the forest. This subgroup brought together investigators with an interest and expertise in managing and analyzing large, heterogeneous datasets with the intent of building systems-level models of cellular functions. The state of the art was discussed and possibilities for community collaborations outlined. A Tutorial titled, "Apples and Oranges: Integrating Disparate Data Sets to Understand Complex Cellular Function" was presented at the American Society for Cell Biology (ASCB) Meeting in San Francisco, CA in December 2005. The following abstract summarizes the tutorial presentation: Systems biology requires the integration of many types of data to understand complex cell processes. Unfortunately, it is currently very difficult to connect disparate data sets. This tutorial provided an overview of software-based approaches to handle heterogeneous data sets, such as proteomics and microarray data. The intent was to discuss the different approaches that are being used, the limitations and advantages of different solutions and where to find help. There will be three areas of discussion: 1) starting with good data, 2) linking data sets, 3) how to find patterns in the data. Both commercial and open source software packages will be discussed, although the emphasis will be on the latter, in particular CCE and Cytoscape. A NCRR Workshop titled, "Separations and Mass Spectrometry Applied to Proteomics and the Informatics Challenges" was planned and executed at PNNL in conjunction with a Proteome Society Meeting hosted by PNNL in April 2005. The following is a description that emphasizes the focus of the workshop: Among the issues confronting the proteomics community, few may be as important as those covered in this workshop. Specifically, we covered both data dissemination standards as well as open source software tools that help analyze that data. Data standards are vital to the growing collaborative nature of large scale proteomics studies in that they will allow multiple institutions located in diverse areas to share the results of instrumental analyses without the requirement that many separate analysis software tools be broadly distributed amongst those groups. Further, standardized formats will simplify publication of analyzed data, fostering rigorous peer review of results and new analysis tool development. Indeed, open source data analysis tool development, wherein the software that enables discovery science as applied to proteomics becomes available to all institutions for use and improvement, was the second major issue covered during the workshop. Rather than requiring collaborators to simply trust the results that stem from black-box style analysis tools, open source software allows any institution to examine, validate, and ultimately, improve these tools when and where appropriate. Lastly, open source tools provide a more solid foundation upon which exciting discoveries may rest. This workshop brought together some of the preeminent individuals working in these areas in an interactive environment to both present their findings and discuss the implications and future directions of these important issues. A Tutorial titled, "Mass Spectrometry-based Quantitative Proteomics for Cell Biology" was presented at the American Society for Cell Biology (ASCB) Meeting in Washington D.C. in December 2004. The following abstract summarizes the tutorial presentation: The effective integration of proteomics data into cell biology studies requires both identification and quantification of the proteins. Mass spectrometry combined with high-resolution liquid chromatographic separations of fractionated or enriched peptide samples represents a highly efficient approach to peptide identification and quantitation. This tutorial will focus on the application of quantitative proteomic strategies (stable isotope labeling and absolute quantitation) in combination with recently developed sample fractionation and enrichment methodologies, including automated protein complex isolation and cell fractionation. The tutorial will include a presentation of the analysis methods for interpreting quantitative proteomics data and their application to analyzing cellular responses to exogenous stimulation. A NCRR Proteomics Workshop titled, "Quantitative Proteomics Applied to Cellular Function" was held in conjunction with the 2004 Northwest Symposium for Systems Biology at PNNL in June 2004. The focus of the workshop was on the evolution of quantitative proteomics. The goals of the workshop were (1) to educate researchers to the utility of the application of quantitative proteomics to understanding cellular function; (2) to stimulate possible new collaborations between the presenters, participating scientists, and the Research Center; and (3) to increase the awareness of the scientific community to the NCRR Biomedical Technology Research Center at PNNL. Research Impact on Biomedical Research and Research Training The challenging collaborative research projects in progress at the PNNL Research Center cover a broad range of biomedical topics important to the community that the Center serves as well as stimulating increased awareness and interest in biomedical research at PNNL. Currently, the Center has subprojects situated with institutes in Belgium, and the Netherlands. The remaining subprojects are situated throughout the U.S.A. from coast to coast. The biomedical importance of this network of collaborative research projects includes the following topics: the investigation of signal transduction pathways and the associated phosphoproteome for quantitative modeling; the characterization of the phosphoproteome of cancer cell lamellipodia; neurite extension and retraction; the urine proteome and kidney transplantation; neural tissue signal transduction and its regulation by a specific phosphatase; CSF and Lyme disease; breast cancer cell enzymatics; the comparative 3D quantitative proteomic profiles of normal and disease model mouse brains; the quantitative proteomics profiling of normal human CSF and CSF from diseased subjects; characterization of pancreatic islet cell growth; prostate cancer; Alzheimer's Disease; enzymatic phosphatase activity in neuroproteomics; CSF proteomics in HIV infection; regulation of hepatic metabolism; the characterization of PTMs in the chromosomal passenger complex; the investigation of post-translational protein modifications related to oxidative stress; the extension of life span; alterations in macrophage lipid raft proteomics; and research on diabetes. Research training has been provided to both new postdoctoral researchers at the Research Center and scientists visiting the Center. Collaborative researchers from laboratories located in California, Texas, Oregon, and Washington visited the Center during this reporting period and received information and/or training. In addition, visiting scientists from institutes located in North Carolina, Texas, Korean University, Seoul National University, and University of Korea have visited the Center during this reporting period for various extended lengths. These visits provide an opportunity to educate other investigators and laboratories on the use of advanced proteomics technologies and the broader national and international research communities on the potential applications of proteome analysis technologies in biomedical and biochemical research.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目及 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 为生物医学界提供先进的蛋白质组学技术是该研究中心的长期目标。 这种信息传递是通过 NCRR 网站（研究进展报告第 26 页网站上的详细信息）以及举办研讨会和教程来实现的。 自 NCRR 项目建立以来，该中心已组织了两次 NCRR 研讨会并参加了六次短期课程/教程。 2009 年 2 月在加利福尼亚州圣地亚哥举行的美国 HUPO 会议上开设了题为“基于 LC-MS 的蛋白质组学的数据提取和分析”的短期课程。 这是 PNNL NCRR 信息学团队连续第三年举办此邀请课程。 该课程涵盖了使用 LC-MS 分析平台进行定量蛋白质组学的几个方面，包括社区可用的定量方法和软件工具的概述、实验设计的注意事项、LC-MS 数据集中的特征发现以及对已识别的肽和肽的统计合理分析。蛋白质。 这些主题旨在告知研究人员在设计 LC-MS 实验时需要考虑的问题，同时还描述用于从 LC-MS 数据中提取信息内容的一般方法。 出席的 15 名人员每人收到一张数据盘 (DVD)，其中包含该中心开发的蛋白质组学软件的软件安装程序，以及用于准备演示的示例数据。 2008 年 3 月在马里兰州贝塞斯达举行的美国 HUPO 会议上开设了题为“基于 LC-MS 的蛋白质组学的数据提取和分析”的短期课程。 该课程涵盖了使用 LC-MS 分析平台进行定量蛋白质组学的几个方面，包括社区可用的方法和软件工具的比较、实验设计的考虑因素、LC-MS 数据集中的特征发现以及对已识别的肽和肽的统计合理分析。蛋白质。 这些主题旨在告知研究人员在设计 LC-MS 实验时需要考虑的问题，同时还描述用于从 LC-MS 数据中提取信息内容的一般方法。 约 35 名与会者收到了一张数据盘 (DVD)，其中包含 PNNL 开发的蛋白质组学软件的软件安装程序，以及用于准备演示中所示图表的示例数据。 2007 年 3 月在华盛顿州西雅图举行的美国 HUPO 会议上开设了题为“基于 LC-MS 的蛋白质组学的数据提取和分析”的短期课程。 该课程旨在教育美国蛋白质组学界，并讨论使用两种不同的 LC-MS 数据提取和分析平台来演示如何将高质量测量精度质谱和高分辨率液相色谱应用于更高通量的蛋白质组学。 提出的主题包括 1) LC-MS 特征提取，2) 大型 LC-MS 数据集的实验设计和分析，以及 3) 使用 LC-MS 鉴定和表征肽和蛋白质。 这些主题旨在从定制和商用 LC-MS 系统中的 LC-MS 实验中获取更多信息内容。 描述了许多信息学工具和算法，其中许多是开源的或可在 NCRR 网站上免费获得。 还向与会者分发了一张包含软件安装程序和演示数据的 DVD。 2006 年 12 月，在加利福尼亚州圣地亚哥举行的美国细胞生物学学会 (ASCB) 会​​议上，召开了一个题为“管理系统生物学中的数据爆炸”的特别兴趣小组。 以下摘要总结了 ASCB 会议上的特殊兴趣小组，题为：基因组学、蛋白质组学和定量成像的新技术正在产生大量数据，有望在未来几十年内彻底改变生物学。 然而，为了实现这一潜力，必须开发新的方法来操纵、集成和分析这些技术可以生成的大型数据集。 否则，树木将继续遮蔽森林。 该小组汇集了对管理和分析大型异构数据集感兴趣并具有专业知识的研究人员，旨在构建细胞功能的系统级模型。 讨论了最新技术并概述了社区合作的可能性。 2005 年 12 月在加利福尼亚州旧金山举行的美国细胞生物学学会 (ASCB) 会​​议上发表了题为“苹果和橙子：整合不同数据集以了解复杂细胞功能”的教程。 以下摘要总结了教程演示：系统生物学需要整合多种类型的数据来理解复杂的细胞过程。 不幸的是，目前连接不同的数据集非常困难。 本教程概述了处理异构数据集（例如蛋白质组学和微阵列数据）的基于软件的方法。 目的是讨论正在使用的不同方法、不同解决方案的局限性和优点以及在哪里寻求帮助。 将讨论三个领域：1）从好的数据开始，2）链接数据集，3）如何找到数据中的模式。 将讨论商业和开源软件包，但重点是后者，特别是 CCE 和 Cytoscape。 2005 年 4 月，与 PNNL 主办的蛋白质组学会会议一起，在 PNNL 策划并举办了题为“应用于蛋白质组学和信息学挑战的分离和质谱分析”的 NCRR 研讨会。 以下是强调研讨会重点的描述： 在蛋白质组学界面临的问题中，很少有像本次研讨会所涵盖的问题那么重要。 具体来说，我们涵盖了数据传播标准以及有助于分析数据的开源软件工具。 数据标准对于大规模蛋白质组学研究日益增长的协作性质至关重要，因为它们将允许位于不同领域的多个机构共享仪器分析的结果，而不需要在这些组中广泛分布许多单独的分析软件工具。 此外，标准化格式将简化分析数据的发布，促进对结果的严格同行评审和新分析工具的开发。 事实上，开源数据分析工具的开发是研讨会期间讨论的第二个主要问题，其中将发现科学应用于蛋白质组学的软件可供所有机构使用和改进。 开源软件不要求合作者简单地信任来自黑盒式分析工具的结果，而是允许任何机构在适当的时间和地点检查、验证并最终改进这些工具。 最后，开源工具为令人兴奋的发现奠定了更坚实的基础。 本次研讨会汇集了这些领域的一些杰出人士，在互动环境中展示他们的发现并讨论这些重要问题的影响和未来方向。 题为“基于质谱的细胞生物学定量蛋白质组学”的教程于 2004 年 12 月在华盛顿特区举行的美国细胞生物学学会 (ASCB) 会​​议上发表。 以下摘要总结了教程演示：将蛋白质组数据有效整合到细胞生物学研究中需要对蛋白质进行鉴定和定量。 质谱法与分级或富集肽样品的高分辨率液相色谱分离相结合，代表了一种高效的肽鉴定和定量方法。 本教程将重点介绍定量蛋白质组学策略（稳定同位素标记和绝对定量）与最近开发的样品分级分离和富集方法相结合的应用，包括自动蛋白质复合物分离和细胞分级分离。 本教程将介绍用于解释定量蛋白质组学数据的分析方法及其在分析细胞对外源刺激反应中的应用。 2004 年 6 月，题为“应用于细胞功能的定量蛋白质组学”的 NCRR 蛋白质组学研讨会与 PNNL 的 2004 年西北系统生物学研讨会同时举行。 研讨会的重点是定量蛋白质组学的发展。 研讨会的目标是（1）教育研究人员如何利用定量蛋白质组学来了解细胞功能； (2) 促进演讲者、参与科学家和研究中心之间可能的新合作； (3) 提高科学界对 PNNL NCRR 生物医学技术研究中心的认识。 研究对生物医学研究和研究培训的影响 PNNL 研究中心正在进行的具有挑战性的合作研究项目涵盖了对该中心所服务的社区非常重要的广泛生物医学主题，并激发了人们对 PNNL 生物医学研究的认识和兴趣。 目前，该中心的子项目位于比利时和荷兰的研究所。 其余子项目遍布美国各地。 该合作研究项目网络的生物医学重要性包括以下主题：信号转导途径的研究和用于定量建模的相关磷酸蛋白质组；癌细胞板状伪足磷酸化蛋白质组的表征；神经突伸展和收缩；尿液蛋白质组和肾移植；神经组织信号转导及其特定磷酸酶的调节；脑脊液和莱姆病；乳腺癌细胞酶学；正常小鼠大脑和疾病模型小鼠大脑的 3D 定量蛋白质组图谱比较；正常人脑脊液和患病受试者脑脊液的定量蛋白质组学分析；胰岛细胞生长的表征；前列腺癌；阿尔茨海默病；神经蛋白质组学中的酶促磷酸酶活性； HIV 感染中的脑脊液蛋白质组学；肝脏代谢的调节；染色体乘客复合体中 PTM 的表征；与氧化应激相关的翻译后蛋白质修饰的研究；延长寿命；巨噬细胞脂筏蛋白质组学的改变；和糖尿病研究。 为研究中心的新博士后研究人员和访问该中心的科学家提供了研究培训。 来自加利福尼亚州、德克萨斯州、俄勒冈州和华盛顿州实验室的合作研究人员在本报告期内访问了该中心并接受了信息和/或培训。 此外，来自北卡罗来纳州、德克萨斯州、韩国大学、首尔国立大学和韩国大学的研究机构的客座科学家在本报告期内对中心进行了不同程度的长时间访问。 这些访问提供了一个机会，让其他研究人员和实验室了解先进蛋白质组学技术的使用，并让更广泛的国内和国际研究界了解蛋白质组分析技术在生物医学和生化研究中的潜在应用。