Algorithms and Software for Protein-Family De Novo Sequencing

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。该项目将开发通过串联质谱法进行从头肽测序的算法和软件，利用两个目前尚未开发的信息渠道：蛋白质家族同源性和同一肽的多个互补光谱。同源性将允许从头测序程序限制注意肽适合某些基序或约束。在严格的约束条件下，该程序将只搜索已知序列中最可能的突变，但在宽松的约束条件下，该程序将像目前的从头测序程序一样广泛搜索。互补光谱，例如，一个CID（碰撞诱导离解）和一个ETD（电子转移离解）光谱，给出了更完整的碎片化，更重要的是，帮助程序识别哪些峰对应于哪些离子类型，例如，有助于区分b离子和y离子。该项目生产的新软件将立即用于抗体和毒素的测序。该项目的具体目标是：同源性引导候选肽的生成，多重和互补光谱的利用（用于候选肽的生成和评分），以及多克隆血清抗体和蜗牛和蜘蛛毒素复杂混合物测序软件的应用和部署。这些都是高价值的靶标，因为抗体对艾滋病毒有反应，毒素作为研究离子通道的探针和药物线索都很有价值。如果该项目达到其目标，未知肽的精确测序将变得比现在容易得多，世界各地的实验室将利用新的数据采集和分析策略，生物医学发现将大大加快。

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 de novo peptide sequencing by tandem mass spectrometry, taking advantage of two currently unexploited information channels: protein family homology, and multiple complementary spectra of the same peptide. Homology will allow the de novo sequencing program to limit attention to peptides fitting certain motifs or constraints. With strict constraints, the program would search only the most likely mutations of known sequences, but with loose constraints the program would search as widely as current de novo sequencing programs. Complementary spectra, for example, one CID (collision-induced dissociation) and one ETD (electron-transfer dissociation) spectrum, give more complete fragmentation, and more importantly, help the program recognize which peaks correspond to which ion types, for example, helping to distinguish b-ions from y-ions. New software produced by the project will be put to immediate use in sequencing antibodies and toxins. The specific aims of the project are: homology-guided generation of candidate peptides, utilization of multiple and complementary spectra (for both candidate generation and scoring), and application and deployment of the software for sequencing polyclonal serum antibodies and complex mixtures of snail and spider toxins. These are high-value targets because the antibodies are reactive to HIV, and the toxins are valuable both as probes to study ion channels and also as pharmaceutical leads. If the project achieves its aims, exact sequencing of unknown peptides will become much easier than it is today, laboratories worldwide will take advantage of the new data acquisition and analysis strategies, and biomedical discovery will be greatly accelerated. PUBLIC HEALTH RELEVANCE: The proposed project is important to public health because it will enable exact identification of unknown, unsequenced proteins, including spider and snail toxins and polyclonal antibodies captured from human serum. Snail toxins are already the basis for FDA-approved analgesics. Captured antibodies could enable antibody treatments for HIV infection and other diseases. .