GPU-accelerated Peptide Search

GPU 加速的肽搜索

• 批准号: 8201122
• 负责人: Brian Pratt
• 金额: $ 20.36万
• 依托单位: INSILICOS
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-08-12 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8201122
• 关键词: Amino Acid Sequence; Area; Biological; Computer Analysis; Computer software; Computers; Data Set; Devices; Discipline; Elements; Environment; Future; Laboratories; Mass Spectrum Analysis; Methods; Peptide Hydrolases; Peptide Sequence Determination; Peptides; Performance; Post-Translational Protein Processing; Process; Proteins; Proteome; Proteomics; Public Health; Qualifying; Research; Research Personnel; Resolution; Resources; Running; Shotguns; Solutions; Speed; Techniques; Trypsin; Work; cluster computing; computer cluster; cost; experience; falls; improved; instrument; interest; laptop; open source; operation; programs; prototype; research study; supercomputer

DESCRIPTION (provided by applicant): The use of Graphics Processing Unit (GPU) devices is proposed to increase the speed of peptide search by as much as an order of magnitude. Peptide search engines perform the most computation-intensive task in shotgun proteomics. This proposal is to speed up peptide search using the increasingly popular approach of general-purpose computation on highly-parallel GPU devices. Computation using GPUs to gain "desktop supercomputer" performance at low cost is an active and fruitful area of research. This project will obtain these benefits for peptide search. As a result, researchers will be able to take experiments that today must be analyzed on a computer cluster, and instead analyze them on their desktop computer. PUBLIC HEALTH RELEVANCE: A enhancement to the popular peptide search engine X!Tandem is proposed, to allow it to run in parallel on graphics processing unit (GPU) cards with dramatically faster performance. This will allow much faster and less-expensive operation, allowing proteomics researchers to analyze large proteomics experiments or search for post- translational modifications (PTMs) using their existing desktop computer. Proteomics has led to many important advances in biological understanding. Yet, many valuable data sets are not searched for PTMs, simply because the computer power necessary to conduct the searches is not available. With this project, we plan to substantially reduce the computational cost of proteomics experiments, via a peptide search engine making use of inexpensive, highly parallel GPU hardware. Thus, this project, if successful, will allow proteomics to be more successfully exploited for public health. The research team is well-qualified to undertake this research, having extensive, direct experience in all the scientific disciplines and specific software elements necessary. The research team includes experts in proteomics, mass spectrometry, peptide search, and GPU computing.

描述（由申请人提供）：提出使用图形处理单元（GPU）设备来将肽搜索的速度提高多达一个数量级。肽搜索引擎在鸟枪蛋白质组学中执行计算密集型任务。这个建议是为了加快肽搜索使用越来越流行的方法，通用计算的高度并行GPU设备。使用GPU以低成本获得“桌面超级计算机”性能的计算是一个活跃且富有成果的研究领域。本项目将为多肽搜索带来这些好处。因此，研究人员将能够进行今天必须在计算机集群上进行分析的实验，而不是在台式计算机上进行分析。 公共卫生相关性：增强流行的肽搜索引擎X！Tandem的提出，使其能够在图形处理单元（GPU）卡上并行运行，具有更快的性能。这将允许更快、更便宜的操作，使蛋白质组学研究人员能够使用现有的台式计算机分析大型蛋白质组学实验或搜索翻译后修饰（PTM）。蛋白质组学在生物学理解方面取得了许多重要进展。然而，许多有价值的数据集没有搜索PTM，仅仅是因为进行搜索所需的计算机能力不可用。在这个项目中，我们计划通过利用廉价、高度并行的GPU硬件的肽搜索引擎来大幅降低蛋白质组学实验的计算成本。因此，该项目如果成功，将使蛋白质组学更成功地用于公共卫生。该研究团队完全有资格进行这项研究，在所有科学学科和必要的特定软件元素方面拥有广泛的直接经验。研究团队包括蛋白质组学、质谱、肽搜索和GPU计算方面的专家。