Complete Human Peptide- and MRM-Atlas

描述(申请人提供)：个性化药物将依赖于分子签名来匹配合适的患者和合适的药物，首先是在临床试验中，然后是在临床实践中。个性化医疗是信息技术、科学和临床治疗协同整合以改善健康和患者福祉的一种新范式。这种方法需要异常庞大的数据库，将分子和临床数据联系起来，这样就可以主动选择患者进行最合适的治疗。为了实现个性化医学，开始开发灵敏和可靠的分析方法来定量检测基因表达、代谢物和蛋白质的变化和分布的三体特征是至关重要的。对于蛋白质，我们必须测量体内平衡或异常分布，以帮助定义当前的健康状态或疾病状态。我们建议的具体、简单和直接的目标是开发一个完整的蛋白质组中心数据库，以便通过使用多反应监测(MRM)对任何感兴趣的人类蛋白质(S)进行有针对性的分析。我们将开发和提供一个蛋白质类型的多肽片段数据库，每个人类蛋白质编码基因至少有4个多肽，以及经过验证的基于MRM的快速和准确的质谱分析，以明确地识别和定量大量样本中的任何人类蛋白质组的蛋白质。根据严格的标准，人类蛋白质编码基因的估计数量为20,332个，但可能高达25,000个。我们的方法包括建立一个全面的、公开可用的数据库，供用户查询和下载快速针对血浆或其他人体组织中感兴趣的蛋白质进行有针对性的分析所需的所有信息。此外，这项工作提供了一个经过验证的蛋白质型多肽数据库，用于设计多肽表位捕获试剂(例如抗体)，以进一步推动该技术的灵敏度比目前~1-10 ng/mL的仪器限值低至少2个数量级。通过使用ISB开发的人类多肽图谱，这是一种高度精选的蛋白质型多肽汇编，其中包括人类蛋白质和其他物种的所有现有质谱学数据，目前正在努力建立一个全面的核磁共振图谱，其中载有关于多肽和多肽片段质量、碎裂倾向以及成功应用多重定量分析所使用的标准化仪器条件的完整信息。根据我们的提议，将使用通过多肽图谱和蛋白质型多肽预测软件确定的蛋白质型多肽生产少量多肽(每种人体蛋白4个多肽)，以建立一个全面的磁共振图集，其中将包含所有相关的多肽生物物理信息、裂解信息、仪器条件以及与一些有效分析的链接，所有这些都将在两年的时间框架内完成。现在是创建完整的人类蛋白质组MRMAtlas的时候了。这无疑将加速开发灵敏可靠的检测方法，用于癌症和其他人类疾病的早期发现、治疗评估和预后评估。 公共卫生相关性：蛋白质组学、基因组学、代谢组学和临床数据的协同结合将通过提高诊断能力、预后准确性和开发新的、个性化的治疗方法，为个性化药物铺平道路。我们的目标是实施最先进的蛋白质组学技术，以获得独特的完整的人类蛋白质组学纲要，用于以多种方式靶向和定量任何人类蛋白质。我们的最终目标是将这一独特的靶向蛋白质组学数据库与基因组和临床数据库相结合，从而提供宝贵的国家资源，加速当前开发基于高度敏感和靶向的蛋白质组学分析方法的努力，用于研究人类疾病，以提供更好的患者护理。

DESCRIPTION (provided by applicant): Personalized medicine will depend on molecular signatures to match the right patients to the right drugs, first in clinical trials, then in clinical practice. Personalized medicine is a new paradigm in which information technology, science, and clinical treatment are synergistically integrated to improve health and patient well-being. This approach requires unusually large databases, relating both molecular and clinical data, such that patients can be proactively selected for the most appropriate therapies. Towards achieving personalized medicine, it is crucial to begin developing sensitive and reliable assays to quantitatively detect the tri-omic signatures of gene expression, metabolite and protein changes and distribution. For proteins, we must measure the homeostatic or aberrant distribution in order to help define the current health status or disease state. The specific, simple and immediate goal of our proposal is to develop a complete proteome centric database to allow the targeted analysis of any human protein(s) of interest through the use of multiple-reaction- monitoring (MRM). We will develop and provide a proteotypic peptide fragmentation database, of at least 4 peptides per human protein-coding gene, with verified rapid and accurate MRM based mass spectrometric assays to unambiguously identify and quantify any protein of the human proteome in a multitude of samples. The estimated number of human protein-coding genes is 20,332 based on strict criteria, but can be as high as 25,000. Our approach involves building a comprehensive, publicly available database for users to query and download all the information required to rapidly implement targeted assays against proteins of interest in plasma or other human tissues. In addition, this effort provides a verified proteotypic peptide database for designing peptide-epitope capture reagents (e.g., antibodies) to further drive the sensitivity of the technique at least 2 orders of magnitude lower than the current instrumental limits of ~1-10 ng/mL. Through the use of the ISB-developed human PeptideAtlas, a highly curated proteotypic peptide compendium of all available mass spectrometry data of human proteins as well as other species, efforts are underway for the building of a comprehensive MRMAtlas that contains complete information on the peptide and peptide fragment mass, fragmentation propensity as well as standardized instrumental conditions to employ for successful application of multiplexed quantitative assays. For our proposal, production of small quantities of peptides (~4 peptides per human protein) based on the proteotypic peptides identified through PeptideAtlas and proteotypic peptide predictability software will be used to build a comprehensive MRMAtlas that will contain all the relevant peptide biophysical information, fragmentation information, instrumental conditions, as well as links to some validated assays, all completed in a 2-year time frame. The time is right to create the complete human proteome MRMAtlas. This will undoubtedly accelerate efforts to develop sensitive and reliable assays for early detection, therapy assessment and prognosis evaluation for cancer as well as other human diseases. PUBLIC HEALTH RELEVANCE: The synergistic combination of proteomics, genomics, metabolomics and clinical data will pave the path to personalized medicine by improving diagnostic capabilities, prognostic accuracy, and the development of new, individually tailored therapeutics. We aim to implement state-of-the-art proteomics technology to acquire a unique complete human proteomics compendium for targeting and quantitating any human protein in a multiplexed manner. Our ultimate goal is to integrate this unique targeted proteomics database with genomic and clinical databases, thus providing an invaluable national resource that will expedite current efforts to develop highly sensitive and targeted proteomics-based assays for studying human disease to provide better patient care.