Center for Computational Mass-Spectrometry

计算质谱中心

• 批准号: 8710893
• 负责人: Pavel A Pevzner
• 金额: $ 106.02万
• 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 2014-09-19
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8710893
• 关键词: Address; Affect; Algorithms; Antibiotics; Antibodies; Area; Award; Bacteria; Bioinformatics; Biological; Biological Markers; Biotechnology; Blood Clot; Blood coagulation; Books; Cataract; Chimeric Proteins; Collaborations; Commit; Communities; Complex; Computational Technique; Computer software; Data; Databases; Development; Education; Educational Activities; Evolution; Filtration; Funding; Gene Expression Profile; Generations; Genes; Genome; Genomics; Germany; Goals; Grant; High Performance Computing; Human Genome; Institutes; Institution; International; Joints; Language; Lead; Letters; Malignant Neoplasms; Mass Spectrum Analysis; Methods; Mutation; Pathway interactions; Peptides; Pharmaceutical Preparations; Positioning Attribute; Post-Translational Protein Processing; Postdoctoral Fellow; Protein Databases; Proteome; Proteomics; Publishing; Research; Research Activity; Research Infrastructure; Research Personnel; Research Project Grants; Resources; Scientist; Sequence Alignment; Singapore; Site; Snake Venoms; Software Engineering; Software Tools; Solutions; Spain; Speed; Staging; Students; Sweden; Systems Biology; Techniques; Technology; Time; Training; Translations; Trees; Uncertainty; United Kingdom; University Hospitals; Work; Writing; aged; anticancer research; base; cancer proteomics; computer science; computerized tools; computing resources; design; experience; improved; infancy; influenza virus vaccine; insertion/deletion mutation; instrument; instrumentation; ion mobility; meetings; novel strategies; programs; prototype; software development; spelling; symposium; tool

This application seeks support for a center of excellence in computational mass spectrometry and a national and international resource in the broad area of proteomics. It proposes to enlarge the current research activities, to branch into previously unexplored areas of computational proteomics, and to support multiple collaborative efforts. The proposal addresses the computational bottleneck that affects the entire proteomics community and impairs interpretation of data in thousands of experimental labs around the world. The goal is to bring the modern algorithmic technologies to mass-spectrometry and to build a new generation of reliable open access software tools to support both new development in mass-spectrometry instrumentation and the emerging applications of mass-spectrometry. The proposal focuses on four directions: (i) enabling complex mass spectrometry searches, (ii) analyzing unknown proteomes without protein databases, (iii) analyzing altered proteomes, and (iv) constructing proteogenomic annotations and analyzing pathways. These directions cover both well-studied but still inadequately addressed problems (like search for mutations and post-translational modifications) and unexplored problems for which there are no computational tools currently available (like antibody sequencing or analyzing fusion proteins in cancer). These projects require two-way collaborative efforts on a wide range of topics involving biomedical and computational scientists from various institutions. While many collaborations have been already established at San Diego (UCSD and Burnham Institute), sixteen other US universities, hospitals and biotechnology companies, as well as foreign research institutions at Germany, Singapore, Spain, Sweden, and United Kingdom, we propose to further extend these collaborations by developing robust open access mass spectrometry software that will catalyze the exchanges between experimental and computational researchers in proteomics. The biomedical applications addressed in these collaborative projects include but are not limited to (i) discovery of cancer biomarkers, (ii) elucidation of changes in aged cataractous lens, (iii) understanding how bacteria adjust to antibiotics and other harsh conditions, (iv) addressing the need to constantly reformulate the influenza vaccine to make it efficient, and (v) sequencing of snake venoms that proved instrumental in design of blood clotting drugs. Educational activities in the area of computational proteomics will also be developed, including short courses, a seminar program, an annual conference, and concerted education of students and postdocs.

该应用程序寻求支持计算质谱卓越中心和国家 和蛋白质组学广泛领域的国际资源。它建议扩大当前的研究 活动，分支到以前未开发的计算蛋白质组学领域，并支持多个 协作努力。该提案解决了影响整个的计算瓶颈 蛋白质组学社区并损害了世界上成千上万的实验实验室中对数据的解释。 目的是将现代算法技术带入质量光谱法并建立新的 生成可靠的开放访问软件工具，以支持质谱法中的新开发 仪器和质量光谱法的新兴应用。该提案重点是四个 方向：（i）启用复杂的质谱搜索，（ii）分析未知蛋白质组没有 蛋白质数据库，（iii）分析改变的蛋白质组，（iv）构建蛋白质组学注释和 分析途径。这些指示涵盖了两个研究，但仍然不足以解决问题 （例如搜索突变和翻译后修改）以及未探索的问题 目前没有计算工具（例如癌症中的抗体测序或分析融合蛋白）。 这些项目需要在涉及生物医学和的广泛主题上进行双向合作努力 来自各个机构的计算科学家。尽管已经建立了许多合作 在圣地亚哥（UCSD和Burnham Institute），其他十六所美国大学，医院和生物技术 公司以及德国，新加坡，西班牙，瑞典和联合的外国研究机构 王国，我们建议通过开发强大的开放访问质量进一步扩展这些合作 光谱软件将催化实验和计算之间的交流 蛋白质组学研究人员。这些协作项目中涉及的生物医学应用程序包括，但 不限于（i）发现癌症生物标志物，（ii）阐明白内障晶状体的变化，（iii） 了解细菌如何适应抗生素和其他恶劣条件，（iv）解决需要 不断重新重新重新重新重新复产流感疫苗以使其有效，（v）蛇毒液的测序 事实证明，在血液凝结药物的设计方面具有重要作用。计算领域的教育活动 还将开发蛋白质组学，包括短课程，研讨会计划，年度会议和 学生和博士后的协调教育。