Center for Computational Mass Spectrometry

计算质谱中心

• 批准号: 8930716
• 负责人: Vineet Bafna
• 金额: $ 135.04万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-20 至 2019-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8930716
• 关键词: Acetylation; Address; Adoption; Algorithmic Software; Algorithms; Antibiotics; Antibodies; Antibody Repertoire; Archives; Area; Biological; Biological Factors; Biological Markers; Cancer Patient; Cataract; Chemicals; Clinical; Communicable Diseases; Communities; Complex; Computer software; DNA Sequence; Data; Databases; Dental caries; Development; Drug Targeting; Drug toxicity; Emerging Technologies; Fingerprint; Generations; Genes; Genome; Genomics; Goals; Guanine Nucleotide Exchange Factors; Health; Histone Code; Histones; Human; Human Microbiome; Industry; Infection; Institution; Libraries; Link; Malignant Neoplasms; Mass Spectrum Analysis; Mining; Monoclonal Antibodies; Mutation; Oncogenes; Peptides; Post-Translational Protein Processing; Protein Isoforms; Proteins; Proteome; Proteomics; Protocols documentation; Research; Scientist; Services; Software Tools; Students; System; Techniques; Technology; Therapeutic; Therapeutic antibodies; Tissues; Training; base; biomedical scientist; breast cancer vaccine; combinatorial; computerized tools; drug discovery; human disease; improved; instrument; instrumentation; lens; microbial; next generation; next generation sequencing; novel; novel therapeutics; oral microbiome; polyclonal antibody; protein aminoacid sequence; protein protein interaction; research and development; response; success; tool; vaccine trial

DESCRIPTION: Mass spectrometry is based on fragmenting biological molecules into smaller pieces, and using the fragment masses as a fingerprint for identifying and quantifying bio-molecules. It is the dominant technology for studying active molecules in healthy and diseased tissue, and identifying protein targets and natural products for novel therapeutics. When the initial proposal Center for Computational Mass Spectrometry (CCMS) was submitted in 2007, the lack of adequate computational tools for analyzing mass spectrometry data was the the key bottleneck. With great success in enabling applications of new experimental techniques such as FTMS, ETD, HCD, top-down mass spectrometry, and many others, the mandate of CCMS continues to be the development of next generation computational technologies and to apply them to open experimental. In this proposal, we will capitalize on our recent results in diverse subfields of computational proteomics and will further branch into previously unexplored MS applications. We will focus specifically on bridging proteomics and genomics technologies using 6 technology research and development platforms. Specifically, we will (a) apply proteogenomics approach for the discovery of abberant cancer genes and analyzing antibody repertoires; (b) sequence natural antibiotics; (c) collate spectral data through spectral archives and networks; (d) develop universal tools for peptide identification; (e) develop tools for top-down proteomics; and, (f) analyzing multiplexed spectra. The technology platforms are driven by a multitude of col- laborative biomedical studies where the use of CCMS developed tools is essential for their success. These studies include (a) unraveling the combinatorial histone code in human diseases; (b) a proteogenomics approach to studies of oral microbiome and polybacterial infections; (c) detecting inter-species chemical in- teractions; (d) developing a systems approach towards the therapeutic modulation of the acetylome ; (e) developing tools for monoclonal and polyclonal antibody sequencing; (f) development of breast cancer vac- cines; (g) clinical cancer proteogenomics; (h) discovery of lantibiotics; (i) discovering proteomic biomarkers for drug toxicity in cancer patients; and, (j) identifying protein-protein interactions and post-translational mod- ifications in cataractous lens. These projects require three-way collaborative efforts on a wide range of topics involving biomedical scientists, mass spectrometrists, and computational scientists from various institutions. CCMS will also train students and practicing scientists from all over the world in computational proteomics, and educate the proteomics community about modern computational mass spectrometry to encourage its wide adoption.

产品说明：质谱法是基于将生物分子破碎成更小的碎片，并使用碎片质量作为指纹来识别和量化生物分子。它是研究健康和患病组织中的活性分子，以及鉴定新疗法的蛋白质靶点和天然产物的主导技术。当计算质谱中心（CCMS）于2007年提交初始提案时，缺乏足够的计算工具来分析质谱数据是关键瓶颈。随着FTMS、ETD、HCD、自上而下质谱等新实验技术的应用取得巨大成功，CCMS的任务仍然是开发下一代计算技术，并将其应用于开放实验。在这个建议中，我们将利用我们最近在计算蛋白质组学的不同子领域的结果，并将进一步分支到以前未开发的MS应用。我们将专注于使用6个技术研发平台来连接蛋白质组学和基因组学技术。具体而言，我们将（a）应用蛋白质基因组学方法发现异常癌症基因和分析抗体库;（B）测序天然抗生素;（c）通过光谱档案和网络整理光谱数据;（d）开发肽鉴定的通用工具;（e）开发自上而下的蛋白质组学工具;以及（f）分析多重光谱。这些技术平台是由大量的合作生物医学研究驱动的，其中使用CCMS开发的工具对其成功至关重要。这些研究包括（a）解开人类疾病中的组合组蛋白密码;（B）研究口腔微生物组和多细菌感染的蛋白质基因组学方法;（c）检测物种间的化学相互作用;（d）开发乙酰组的治疗调节的系统方法;（e）开发用于单克隆和多克隆抗体测序的工具;（f）开发乳腺癌疫苗;（f）开发抗肿瘤药物;（g）开发抗肿瘤药物;（f）开发抗肿瘤药物。（g）临床癌症蛋白质基因组学;（h）羊毛硫抗生素的发现;（i）发现蛋白质组学 癌症患者中药物毒性的生物标志物;和（j）鉴定白内障透镜中的蛋白质-蛋白质相互作用和翻译后修饰。这些项目需要三方合作，涉及来自不同机构的生物医学科学家，质谱学家和计算科学家的广泛主题。CCMS还将在计算蛋白质组学方面培训来自世界各地的学生和实践科学家，并教育蛋白质组学社区了解现代计算质谱，以鼓励其广泛采用。