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

作为目前五个CPTAC PCC之一，我们建议利用我们已建立的中心来进一步开展研究 在对来自人类的生物样本和其他癌症的临床前模型进行全面表征方面， 类型我们组建了一支由基础和临床科学家组成的优秀团队， 以及使用基因蛋白质组学方法与癌症进展相关的蛋白质修饰。这 多学科团队将由相同的三名主要研究者（PI）管理，包括 国际公认的蛋白质组学技术、基因组学、蛋白质组学特定生物信息学、 生物统计学、肿瘤学、病理学、癌症生物学、检测开发、质量控制、技术优化， 和临床实验室科学/临床化学。我们的团队拥有互补和综合的专业知识， 过去和现在的成功合作。该计划是将基因组学的研究结果与蛋白质组学结合起来， 分析（基因蛋白质组学）并克服全面理解中的注意事项和挑战 肿瘤生物学我们相信，基因组数据提供了一个非常有价值的分子途径， 基因和途径，可能是有用的检测，鉴别诊断，结果预测， 癌症的治疗靶点。蛋白质组学方法将提供鉴定独特特征的方法， 是蛋白质固有的，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期间验证的技术平台，该技术平台具有高通量、稳健性 这些技术已经过验证，能够在不同的环境中产生可重复的结果。 labs.我们将使用两步策略来表征定义的基因组表征样品集。的 第一步是使用质谱法从生物和临床标本中发现靶蛋白 和基于亲和力的技术。第二步是使用高通量确认这些靶标， CPTAC Tier 2经分析验证的靶向检测试剂盒，例如，多反应监测质谱 光谱法（MRM-MS）。此外，我们还建议开展技术改进试验研究。目标 是使用优化的， 标准化的高通量技术用于发现的目标。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，我们相信， 蛋白质基因组学数据分析和翻译方面的专业知识对于PCC的成功和整个项目的成功至关重要。 CPTAC网络。我们建议的PCC的调查员/PI将成为CPTAC申请的一部分 蛋白基因组数据分析（PGDAC）和转化研究（PTCR）中心。合作与团队 工作是CPTAC计划成功的关键。有了这个多学科的优秀团队的基础和 我们的PCC为临床科学家提供了成功表征生物和临床 发现和确认癌症靶点，以推进精确的癌症医学。

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.