Algorithms and Software for Difficult Proteomics Problems

描述（由申请人提供）：拟议项目的广泛，长期目标是使基于质谱的蛋白质研究成为可能。该项目将开发算法和软件，用于在困难的蛋白质组学样品中鉴定肽，包括严重修饰的样品，其中大多数肽携带一种或多种修饰，以及突变样品，其中许多肽与相应的数据库肽有一个或多个氨基酸取代。一种特别重要的重修饰样品是故意氧化的样品，用于称为“氧化足迹”的技术，以获得蛋白质和复合物的结构信息。对于困难的蛋白质组学样品，目前的肽鉴定程序，如Mascot和SEQUEST，通常给出较弱的结果，并且很少有手段来评估结果的质量。因此，该项目的具体目标是：(1)发展统计技术来衡量修改和突变鉴定的错误发现率；(2)构建氧化足迹识别软件；(3)加快和改进突变和修饰搜索。如果该项目达到目标，生物化学合作者将使用氧化足迹来研究致病菌的抗体-抗原结合，并将对克氏锥虫等高度可变的生物体进行更深入、更彻底的蛋白质组学分析。更广泛地说，全世界从事各种健康相关项目的蛋白质组学实验室将能够分析困难的样本。研究人员将能够获得x射线晶体学或核磁共振无法获得的蛋白质和复合物的结构信息；他们将能够研究低测序和高度可变的生物体；他们将能够通过寻找意想不到的化学修饰来双重检查蛋白质组学分析。公共卫生相关性：拟议项目对公共卫生的重要性在于，它将把蛋白质组学鉴定扩展到更困难的生物样品，例如含有未测序或未测序病原体的样品。提议的工作包括“氧化足迹”的计算工具，这是一种研究蛋白质结合和构象的强大新技术。该技术将使研究病原菌的抗体-抗原结合成为可能；抗原变异是目前研制疫苗的主要障碍之一。

DESCRIPTION (provided by applicant): The broad, long-term objective of the proposed project is to enable mass spectrometry based protein research. The project will develop algorithms and software for peptide identification in difficult proteomics samples, including heavily modified samples, in which most peptides carry one or more modifications, and mutated samples, in which many peptides differ by one or more amino acid substitutions from the corresponding database peptides. One especially important type of heavily modified sample is a deliberately oxidized sample, used in the technique called "oxidative footprinting" to obtain structural information for proteins and complexes. On difficult proteomics samples, the current peptide identification programs, such as Mascot and SEQUEST, generally give weak results, and there is very little means to assess the quality of the results. Thus the specific aims of the project are: (1) to develop statistical techniques to measure false discovery rates for modification and mutation identifications; (2) to build identification software for oxidative footprinting; and (3) to speed up and improve mutation and modification searching. If the project achieves its aims, biochemistry collaborators will use oxidative footprinting to study antibody-antigen binding for pathogenic bacteria, and will perform deeper and more thorough proteomic analyses of highly variable organisms such as Trypanosoma cruzi. More generally, proteomics laboratories worldwide, working on a wide variety of health related projects, will be able to analyze difficult samples. Researchers will be able to obtain structural information on proteins and complexes that are not amenable to x-ray crystallography or NMR; they will be able to study poorly sequenced and highly variable organisms; and they will be able to doublecheck proteomics analyses by searching for unanticipated chemical modifications. PUBIC HEALTH RELEVANCE: The importance of the proposed project to public health is that it will extend proteomics identifications to more difficult biological samples, such as samples containing unsequenced or poorly sequenced pathogens. The proposed work includes computational tools for "oxidative footprinting", a powerful new technique for studying protein binding and conformations. This technique will enable the study of antibody-antigen binding for pathogenic bacteria; variation in antigens is currently one of the major obstacles to the development of vaccines.