PARALLEL MINING OF NEW PEPTIDES FROM WHOLE PROTEOMES

从整个蛋白质组中并行挖掘新肽

• 批准号: 8364217
• 负责人: Jake Yue Chen
• 金额: $ 0.11万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-15 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8364217
• 关键词: Address; Alternative Splicing; Biological; Biomedical Research; Cataloging; Catalogs; Data; Databases; Detection; Exons; Expressed Sequence Tags; Funding; Gene Expression Profile; Genes; Genome; Grant; High Performance Computing; Maps; Messenger RNA; Mining; National Center for Research Resources; Pattern; Peptides; Principal Investigator; Protein Isoforms; Proteins; Proteome; Proteomics; RNA Splicing; Regulator Genes; Reporting; Research; Research Infrastructure; Resources; Sampling; Source; Transcript; United States National Institutes of Health; biological systems; cost; next generation; protein expression

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Protein isoforms are an essential component for expanding functional complexity of the eukaryotic genomes. Current high-throughput studies of protein isoforms take advantage of advances in EST sequencing, exon array, exon-exon junction array, and next-generation sequencing at the mRNA transcript level. Systematic, proteome-scale characterization of protein isoforms directly at the protein/peptide level has not yet been reported. Compared with the indirect transcriptome-level characterizations, direct proteome-level characterization of protein isoforms can address the wide-spread concern that mRNA-level expressions and protein-level expression do not correlate well in a dynamical biological system. This project is motivated by the need for direct proteome-level characterization of protein isoforms to answer the following questions: 1) what genes can these new peptides be mapped to? 2) what are the patterns of alternative splicing or mis-splicing in the proteins found in biological samples of different species? and 3) what are the different gene regulatory mechanism or biological context that caused differential detection of panels of such new peptides? In this project, we propose to comprehensively catalog all hypothetical and functional new peptides characterized for each target proteome available from proteomics raw data in the ProteoCommons.org database (totaling around 21TB).We request approximately 50,000 SUs on Blacklight of PSC, to search for new peptides from these raw proteomics spectral data.

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 蛋白质异构体是扩展真核生物基因组功能复杂性的重要组成部分。目前蛋白质异构体的高通量研究利用了EST测序、外显子阵列、外显子-外显子连接阵列和mRNA转录水平下的下一代测序的进展。直接在蛋白质/肽水平对蛋白质异构体进行系统的蛋白质组规模表征尚未报道。与间接转录组水平表征相比，蛋白质异构体的直接蛋白质组水平表征可以解决广泛关注的问题，即mRNA水平表达和蛋白质水平表达在动态生物系统中不相关。该项目的动机是需要直接蛋白质组水平表征蛋白质异构体，以回答以下问题：1）这些新的肽可以映射到什么基因？2)在不同物种的生物样本中发现的蛋白质中，选择性剪接或错误剪接的模式是什么？以及3）引起这些新肽组的差异检测的不同基因调控机制或生物学背景是什么？在这个项目中，我们建议全面编目所有假设的和功能性的新肽，这些新肽是从ProteoCommons.org数据库中的蛋白质组学原始数据（总计约21 TB）中获得的，针对每个靶蛋白质组进行表征。我们在PSC的Blacklight上请求大约50，000个SU，以从这些原始蛋白质组学光谱数据中搜索新肽。