Quantitative and Qualitative Differential Expression Proteomics

描述（由申请人提供）：食品和药物管理局宣布制定关键路径计划，以解决提交批准的创新医疗产品数量减少的问题。本报告的第一个主题是迫切需要开发新的生物标志物来改善临床试验和改善医学治疗。2007年，杜克大学医学院和基因组科学与政策研究所合作创建了杜克蛋白质组学核心设施，这是一个共享资源设施，其使命是提供蛋白质表征资源和专业知识，以支持杜克大学研究人员的基础和临床研究项目。蛋白质组学核心设施最初的设计是为了提供基于液相色谱-质谱（LC/MS）的蛋白质组学的功能，用于蛋白质鉴定和蛋白质定量，包括生物标志物发现（开放式LC/MS/MS）和生物标志物验证（具有多重反应监测的靶向LC/MS/MS）实验，最近（2009年2月）增加了用于这些生物标志物验证研究的多重抗体检测功能。杜克大学蛋白质组学设施于2007年9月上线，并成功地满足了整个医学院44位主要研究人员的蛋白质组学需求。大多数项目都是差异表达项目，提供各种样品类型的定性和定量信息，包括细胞系、组织裂解物、蛋白质复合物和生物流体。特别相关的是人类临床样本中生物标志物发现实验的成功，这导致了生物标志物发现蛋白质组学项目数量的显著增加。由于2009年有大量的生物标记物发现/验证样本在排队中，这些样本来自已承诺为其分析提供资金的项目（约1,300个LC/MS分析），我们的设施已达到最大容量，由于缺乏LC/MS仪器时间，此类新项目被无限期推迟或拒绝。因此，本S10提案要求一个开放的基因组LC/MS系统，有效地与我们现有的系统相同，以支持本提案中描述的nih资助的研究人员的研究项目。因此，重点是增加我们设施的能力，额外的能力来自仪器平台，我们已经证明了成功的记录，一个已经证明了出色的定量可重复性和足够的系统坚固性，用于临床规模的生物标志物研究，这是实现本提案中描述的研究的研究目标所必需的。

DESCRIPTION (provided by applicant): the Food and Drug Administration announced the development of the Critical Path Initiative in order to address the decreasing numbers of innovative medical products being submitted for approval. The first topic addressed by this report was the pressing need for the development of new biomarkers to improve clinical trials and improve medical therapy. In 2007, the School of Medicine and the Institute for Genome Sciences & Policy at Duke University collaborated to create the Duke Proteomics Core Facility, a shared resource facility with a mission to provide protein characterization resources and expertise in support of the basic and clinical research programs of Duke Investigators. The Proteomics Core Facility was originally designed to provide capabilities for liquid-chromatography-mass spectrometry (LC/MS) based proteomics for protein identification and protein quantitation, including biomarker discovery (open LC/MS/MS) and biomarker verification (targeted LC/MS/MS with multiple reaction monitoring) experiments, and has recently (February 2009) added the capability for multiplexed antibody assays for these biomarker verification studies. The Duke Proteomics Facility came on-line in September 2007, and has successfully served the proteomics needs of 44 Principal Investigators across the School of Medicine. The majority of the projects have been differential expression projects, providing both qualitative and quantitative information on a wide variety of sample types, including cell lines, tissue lysates, protein complexes, and biofluids. Of particular relevance is the success in biomarker discovery experiments in human clinical samples, which has lead to a significant increase in the number of projects submitted for biomarker discovery proteomics. Because of the large number of biomarker discovery/verification samples in the queue in 2009 from projects that have committed funds for their analyses (>1,300 LC/MS analyses), our Facility has reached maximum capacity, with new projects of this type being delayed indefinitely or turned away due to lack of LC/MS instrument time. Therefore, this S10 proposal requests an open 'omic LC/MS system effectively identical to the system we have in place in our facility to support the research projects from NIH-funded investigators described in this proposal. Thus, the focus is on adding capacity to our Facility, with the additional capacity coming from an instrument platform where we have a proven track record of success, one which has demonstrated excellent quantitative reproducibility and sufficient system ruggedness for clinical-scale biomarker studies, as is necessary to achieve the research aims of the studies described in this proposal. PUBLIC HEALTH RELEVANCE: The proposed LC/MS system will significantly increase the capacity of the Duke Proteomics Facility to conduct differential protein expression analyses of biologic materials such as cell and tissue lysates, blood, and other body fluids. The research projects enabled by this proposal aim to advance our understanding of disease areas including oncology, heart disease, liver disease, osteoarthritis, and infectious diseases, and ultimately will improve clinical trials and patient therapies through the discovery and characterization of protein 'biomarkers' of health and disease. This LC/MS system will essentially double the instrument capacity available for such studies at Duke and enable us to leverage the extensive expertise, robust data analysis capabilities, and plethora of important biomedical research opportunities at Duke to the fullest extent.