The Comprehensive Proteome Characterization Center at Johns Hopkins: High Precision Discovery and Confirmation of Genoproteomic Targets

作为目前五个CPTAC项目控制中心之一，我们建议利用我们现有的中心来促进我们的研究 在对附加癌症的人类和临床前模型中的生物旋毛虫的综合表征中 类型。我们已经组建了一支由基础和临床科学家组成的优秀团队来发现和确认蛋白质 以及使用基因蛋白质组学方法进行与癌症进展相关的蛋白质修饰。这 多学科小组将由相同的三名首席调查员(PI)管理，成员包括 国际公认的蛋白质组技术、基因组学、蛋白质组学特定生物信息学专家， 生物统计学、肿瘤学、病理学、癌症生物学、化验发展、质量控制、技术优化 和临床检验科学/临床化学。我们的团队拥有互补和集成的专业知识 之前和正在进行的成功合作。该计划是将基因组学的发现与蛋白质组学结合起来 分析(基因蛋白质组学)和克服在全面理解 肿瘤生物学。我们相信基因组数据为鉴定提供了一个非常有价值的分子途径。 可用于检测、鉴别诊断、结果预测和 癌症的治疗靶点。蛋白质组学方法将提供独特的特征鉴定， 是蛋白质所固有的，包括翻译后修饰，如糖基化和磷酸化。 我们建议使用在当前CPTAC中经过验证的高吞吐量、健壮性的技术平台 和最先进的技术。这些技术都是经过验证的，能够产生可重现的结果 实验室。我们将使用两步策略来描述已定义的基因组特征样本集。这个 第一步是利用质谱学从生物和临床标本中发现目标蛋白。 和基于亲和力的技术。第二步是使用高吞吐量来确认这些目标， CPTAC Tier 2分析验证的靶向分析，例如多反应监测质量 光谱分析(MRM-MS)。此外，我们建议开展技术改进的先导研究。目标是 是使用优化的、可重复性的、灵敏的、定量的和多重的分析 针对已发现目标的标准化高通量技术。虽然这个PCC应用程序的重点是 生物和临床标本的蛋白质组学特征，我们认为理解和 蛋白质组数据分析和翻译方面的专业知识将是专家委员会和整个 CPTAC网络。我们建议的PCC的调查员/PI将成为CPTAC申请的一部分 蛋白质组数据分析(PGDAC)和翻译研究(PTCR)中心。协作和团队 工作是CPTAC计划成功的关键。与这支由杰出的基础和专业人员组成的多学科团队 临床科学家，我们的PCC为成功描述生物学和临床特征提供了最佳机会 发现和确认癌症靶点的标本，以推进精准癌症医学。

As one of the five current CPTAC PCCs, we propose to leverage our established center to further our research in the comprehensive characterization of biospecimens from human and preclinical models for additional cancer types. We have assembled an outstanding team of basic and clinical scientists to discover and confirm proteins and protein modifications associated with cancer progression using genoproteomic approaches. This multidisciplinary team will be managed by the same three Principal Investigators (PI) and consists of internationally recognized experts in proteomic technologies, genomics, proteogenomics-specific bioinformatics, biostatistics, oncology, pathology, cancer biology, assay development, quality control, technology optimization, and clinical laboratory science/clinical chemistry. Our team has complementary and integrated expertise with previous and ongoing successful collaborations. The plan is to integrate the genomics findings with proteomic analysis (genoproteomics) and to overcome the caveats and challenges in the comprehensive understanding of tumor biology. We believe that genomic data provides a highly valuable molecular route towards the identification of genes and pathways that could be useful for the detection, differential diagnosis, outcome prediction and therapeutic targets of cancer. The proteomic approaches will provide the identification of unique features that are inherent to proteins including post-translational modifications, such as glycosylation and phosphorylation. We propose to use the technology platform validated during the current CPTAC which is high throughput, robust and state of the art. These technologies are proven, with the capability of generating reproducible results across labs. We will use a two-step strategy to characterize defined sets of genomically-characterized samples. The first step is the discovery of target proteins from both biological and clinical specimens using mass spectrometry and affinity based technologies. The second step is the confirmation of these targets using high-throughput, CPTAC Tier 2 analytically validated targeted assays, for example, Multiple Reaction Monitoring Mass Spectrometry (MRM-MS). In addition, we propose to develop pilot studies for technology improvement. The goal is to generate accurate, reproducible, sensitive, quantitative, and multiplexed assays using optimized and standardized high-throughput technologies for the discovered targets. While this PCC application is focused on the proteomic characterization of biological and clinical specimens, we believe that the understanding of and expertise in proteogenomic data analysis and translation will be critical for the success of the PCC and the overall CPTAC network. Investigators/PIs from our proposed PCC will be part of applications for the CPTAC Proteogenomic Data Analysis (PGDAC) and Translational Research (PTCR) Centers. Collaboration and team work are key to the success of the CPTAC program. With this multidisciplinary team of outstanding basic and clinical scientists, our PCC offers the best opportunity for the successful characterization of biological and clinical specimens to discover and confirm cancer targets to advance precision cancer medicine.