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倡议，以解决提交审批的创新医疗产品数量不断减少的问题。本报告讨论的第一个主题是迫切需要开发新的生物标记物来改进临床试验和改善医学治疗。2007年，医学院和杜克大学基因组科学与政策研究所合作创建了杜克蛋白质组核心设施，这是一个共享的资源设施，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计划。蛋白质组学核心设施最初旨在为基于液-色-质谱仪(LC/MS)的蛋白质组学提供蛋白质鉴定和蛋白质定量的能力，包括生物标记物发现(开放式LC/MS/MS)和生物标记物验证(具有多反应监测的靶向LC/MS/MS)实验，最近(2009年2月)为这些生物标记物验证研究增加了多重抗体分析的能力。杜克大学蛋白质组学设施于2007年9月上线，并成功地满足了医学院44名首席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，提供了关于各种样本类型的定性和定量信息，包括细胞系、组织裂解物、蛋白质复合体和生物体液。尤其重要的是，在人类临床样本中发现生物标记物的实验取得了成功，这导致提交给生物标记物发现蛋白质组学的项目数量显著增加。由于2009年有大量生物标记物发现/验证样品在排队等待，这些样品来自已承诺为其分析提供资金的项目(&gt；1,300个LC/MS分析)，我们的设施已达到最大容量，这类新项目因缺少LC/MS仪器时间而被无限期推迟或拒绝。因此，这份S10提案要求一个开放的LC/MS系统，有效地与我们设施中的系统完全相同，以支持本提案中描述的NIH资助研究人员的研究项目。因此，重点是增加我们设施的能力，额外的容量来自一个仪器平台，该平台已经证明了出色的定量重复性和足够的系统坚固性，用于临床规模的生物标记物研究，这是实现本提案中所述研究的研究目标所必需的。 公共卫生相关性：拟议的LC/MS系统将显著提高杜克蛋白质组学设施对生物材料(如细胞和组织裂解物、血液和其他体液)进行差异蛋白质表达分析的能力。这项建议促成的研究项目旨在促进我们对疾病领域的了解，包括肿瘤学、心脏病、肝病、骨关节炎和传染病，并最终将通过发现和表征健康和疾病的蛋白质“生物标记物”来改进临床试验和患者治疗。这一LC/MS系统将使杜克大学可用于此类研究的仪器容量增加一倍，并使我们能够最大限度地利用杜克大学丰富的专业知识、强大的数据分析能力和大量重要的生物医学研究机会。

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.