TCP3: QUALITATIVE & QUANTITATIVE PROTEOMIC ANALYSIS OF LYSINE MODIFICATIONS

TCP3：定性

• 批准号: 7724687
• 负责人: AKHILESH PANDEY
• 金额: $ 39.27万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-01 至 2009-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7724687
• 关键词: Acetylation; Amino Acid Sequence; Biochemistry; Bioinformatics; Complex Mixtures; Computer Retrieval of Information on Scientific Projects Database; Cultured Cells; Detection; Extensible Markup Language; Funding; Grant; Head; Human; India; Institutes; Institution; Ions; Lysine; Maps; Mass Spectrum Analysis; Methodology; Methods; Methylation; Modification; Pathway interactions; Peptide Sequence Determination; Peptides; Post-Translational Protein Processing; Protein Databases; Proteins; Proteomics; Relative (related person); Research; Research Personnel; Resources; Sampling; Scanning; Site; Source; Stable Isotope Labeling; Technology; Ubiquitin; United States National Institutes of Health; Yeasts; file format; improved; professor; repository; research study; software development; tool

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Technology Core Projects 3: Quantitative mass spectrometry of protein modifications and detecting protein modifications in complex mixtures - Akhilesh Pandey, Assistant Professor, Dept. of Biological Chemistry and IGM. The aim is to develop quantitative methods for mapping/detecting sites of acetylation, methylation, ubiquitylation and SUMOylation in proteins. In addition, his methods can be routinely applied to protein mixtures by prefractionation (MUDPIT) methodologies. Dr. Pandey also heads a major effort in protein bioinformatics. This involves a critical databasing effort with the Institute of Bioinformatics in Bangalore, India. 1. To develop stable isotope labeling in cell culture (SILAC) method to obtain quantitative information at the protein and peptide level from multiple samples (up to four different states) in a single experiment. This will allow for simultaneous relative quantitation of i) protein abundance in all 4 states, and, ii) post-translational modifications in all 4 states. 2. To develop mass spectrometric methods for improved detection of acetylated, methylated and ubiquitylated peptides. We will develop precursor ion scanning as well as neutral loss scanning methods to selectively identify peptides carrying an acetyl, methyl or ubiquitin moieties from complex mixtures. 3. To develop software tools for analysis of quantitation and to create a repository of all lysine modifications in yeast and humans. To generate pathways involving lysine modifications in a standardized format and to generate mapping of PTMs on the protein sequences in XML file format to enable better searching of protein databases using mass spectrometry-derive

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 技术核心项目3：蛋白质修饰的定量质谱和检测复杂混合物中的蛋白质修饰- Akhilesh Pandey，助理教授，系。生物化学和IGM。其目的是开发定量方法，用于定位/检测蛋白质中乙酰化、甲基化、泛素化和SUMO化位点。此外，他的方法可以通过预分级分离（MUDPIT）方法常规应用于蛋白质混合物。Pandey博士还领导了蛋白质生物信息学方面的一项重大工作。 这涉及印度班加罗尔生物信息学研究所的关键数据库工作。 1.开发细胞培养中稳定同位素标记（SILAC）方法，以在单个实验中从多个样品（最多4种不同状态）中获得蛋白质和肽水平的定量信息。这将允许同时相对定量i）所有4种状态下的蛋白质丰度，和ii）所有4种状态下的翻译后修饰。 2.开发质谱方法，用于改进乙酰化、甲基化和泛素化肽的检测。我们将开发前体离子扫描以及中性损失扫描方法，以选择性地识别肽携带乙酰基，甲基或泛素部分从复杂的混合物。 3.开发定量分析的软件工具，并创建酵母和人类中所有赖氨酸修饰的知识库。以标准化格式生成涉及赖氨酸修饰的途径，并以XML文件格式生成蛋白质序列上的PTM映射，以便使用质谱法更好地搜索蛋白质数据库。