Next-Generation Proteomics: Massively Parallel Single-Molecule Protein Identifica

下一代蛋白质组学：大规模并行单分子蛋白质鉴定

• 批准号: 9117594
• 负责人: EDWARD M MARCOTTE
• 金额: $ 77.25万
• 依托单位: UNIVERSITY OF TEXAS AT AUSTIN
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-30 至 2018-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9117594
• 关键词: Amino Acid Sequence; Antibodies; Biochemical; Biological Assay; Biological Markers; Biology; Biopsy; Blood; Complex Mixtures; DNA; DNA Sequence; Development; Diagnosis; Disease; Fluorescence Microscopy; Gene Expression; Genome; Goals; Individual; Malignant Neoplasms; Massive Parallel Sequencing; Medicine; Methods; Monitor; Mutation; Nucleic Acids; Nucleotides; Pattern; Peptide Sequence Determination; Peptides; Post-Translational Protein Processing; Procedures; Proteins; Proteomics; Reading; Research; Running; Saliva; Sampling; Serum; Technology; Urine; abstracting; base; biomarker discovery; cancer biomarkers; cancer diagnosis; diagnostic biomarker; interest; metaproteomics; molecular diagnostics; next generation; next generation sequencing; protein aminoacid sequence; protein biomarkers; protein expression; protein profiling; sequencing platform; single molecule; success

DESCRIPTION Abstract: The development of next-generation DNA sequencing methods for quickly acquiring genome and gene expression information has transformed biology. The basis of ""next-gen"" DNA sequencing is the acquisition of large numbers of short reads (typically 35-500 nucleotides) in parallel. Currently available single-molecule next-gen sequencing platforms monitor the sequencing of single DNA molecules using fluorescence microscopy, allowing for approx. a billion sequencing reads per run. Unfortunately, no method of similar scale and throughput exists to identify and quantify specific proteins in complex mixtures, representing a critical bottleneck in many biochemical, molecular diagnostic, and biomarker discovery assays. What is urgently needed is a massively parallel method, akin to next-gen DNA sequencing, for identifying and quantifying individual peptides or proteins in a sample. I propose a single-molecule peptide sequencing strategy that will achieve exactly this goal. This will in principle allow billions of distinct peptides to be sequenced in parallel (or at least sequenced sufficiently to provide informative sequence patterns), thereby identifying proteins composing the sample and digitally quantifying them by direct counting of peptides. This transformative approach should enable the quantitative, massively parallel sequencing of proteins. Success of the proposed research wil create a technology suficiently ready for real-world protein sequencing problems. Such an approach would have broad applications across biology and medicine, and could be as fundamental for proteins as, for example, PCR is for nucleic acid research. Potential applications include, for example, profiling of protein expression in normal body niches or in disease, metaproteomics, profiling the circulating serum antibodies, the search for and quantification of protein post-translational modifications, and, of particular interest, identifyin biomarkers relevant to cancer and infectious diseas

描述 摘要： 用于快速获取基因组和基因表达信息的下一代DNA测序方法的发展已经改变了生物学。“下一代”DNA测序的基础是并行获取大量短读取序列(通常为35-500个核苷酸)。目前可用的单分子下一代测序平台使用荧光显微镜监测单DNA分子的测序，允许大约。每次运行10亿次测序读数。不幸的是，没有类似规模和吞吐量的方法来鉴定和定量复杂混合物中的特定蛋白质，这是许多生化、分子诊断和生物标记物发现分析的关键瓶颈。迫切需要的是一种大规模并行的方法，类似于下一代DNA测序，用于识别和量化样本中的单个多肽或蛋白质。我提出了一种单分子多肽测序策略，它将正好实现这一目标。原则上，这将允许对数十亿个不同的多肽进行并行测序(或至少充分测序 以提供信息的序列模式)，从而识别组成样本的蛋白质，并通过直接计数多肽来对其进行数字量化。这种变革性的方法应该能够对蛋白质进行定量的大规模平行测序。这项拟议研究的成功将创造一种足以应对现实世界蛋白质测序问题的技术。这样的方法将在生物学和医学领域有广泛的应用，并可能对蛋白质具有基础性作用，例如，聚合酶链式反应对于核酸研究。潜在的应用包括，例如，在正常身体的利基或疾病中蛋白质表达的图谱，代谢蛋白质组学，循环血清抗体的图谱，蛋白质翻译后修饰的搜索和量化，以及特别感兴趣的识别与癌症和传染病相关的生物标记物。

项目成果

Systematic comparison of variant calling pipelines using gold standard personal exome variants.

• DOI: 10.1038/srep17875
• 发表时间: 2015-12-07
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: Hwang S;Kim E;Lee I;Marcotte EM
• 通讯作者: Marcotte EM

A theoretical justification for single molecule peptide sequencing.

• DOI: 10.1371/journal.pcbi.1004080
• 发表时间: 2015-02
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Swaminathan J;Boulgakov AA;Marcotte EM
• 通讯作者: Marcotte EM

Panorama of ancient metazoan macromolecular complexes.

• DOI: 10.1038/nature14877
• 发表时间: 2015-09-17
• 期刊: NATURE
• 影响因子: 64.8
• 作者: Wan, Cuihong;Borgeson, Blake;Phanse, Sadhna;Tu, Fan;Drew, Kevin;Clark, Greg;Xiong, Xuejian;Kagan, Olga;Kwan, Julian;Bezginov, Alexandr;Chessman, Kyle;Pal, Swati;Cromar, Graham;Papoulas, Ophelia;Ni, Zuyao;Boutz, Daniel R.;Stoilova, Snejana;Havugimana, Pierre C.;Guo, Xinghua;Malty, Ramy H.;Sarov, Mihail;Greenblatt, Jack;Babu, Mohan;Derry, W. Brent;Tillier, Elisabeth R.;Wallingford, John B.;Parkinson, John;Marcotte, Edward M.;Emili, Andrew
• 通讯作者: Emili, Andrew

Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains.

• DOI: 10.1021/pr4011684
• 发表时间: 2014-05-02
• 期刊: JOURNAL OF PROTEOME RESEARCH
• 影响因子: 4.4
• 作者: Kwon, Taejoon;Huse, Holly K.;Vogel, Christine;Whiteley, Marvin;Marcotte, Edward M.
• 通讯作者: Marcotte, Edward M.

Efforts to make and apply humanized yeast.

• DOI: 10.1093/bfgp/elv041
• 发表时间: 2016-03
• 期刊: Briefings in functional genomics
• 影响因子: 4
• 作者: Laurent JM;Young JH;Kachroo AH;Marcotte EM
• 通讯作者: Marcotte EM