INTERNET BASED TOOLS RESOURCE FOR PROTEIN MASS SPECTROMETRY

基于互联网的蛋白质质谱工具资源

• 批准号: 8361488
• 负责人: JULIO C PADOVAN
• 金额: $ 1.04万
• 依托单位: ROCKEFELLER UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-03-01 至 2012-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8361488
• 关键词: Affect; Algorithms; Amino Acid Sequence; Amino Acids; Bioinformatics; Chemicals; Collection; Computational Biology; Cross-Linking Reagents; Databases; Disulfides; Funding; Grant; Internet; Libraries; Manuscripts; Maps; Mass Spectrum Analysis; Methods; Modification; Molecular Biology; National Center for Research Resources; Peptide Mapping; Peptide Sequence Determination; Peptides; Principal Investigator; Probability; Process; Protein Sequence Analysis; Proteins; Proteome; Research; Research Infrastructure; Resources; Retrieval; Source; United States National Institutes of Health; base; cost; crosslink; design; disulfide bond; macromolecule; oxidation; polypeptide; protein aminoacid sequence; tool

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. We continue to maintain an internet based bioinformatic resource for protein mass spectrometry. WE also maintain the databases used to search for proteins and insert specialized databases upon request by our users. These tools ca be found at the universal resource locator http://www.rockefeller.edu/labheads/chait/tools.php and include: ProFound ProFound is a tool for searching a protein sequence collections with peptide mass maps. A Bayesian algorithm is used to rank the protein sequences in the database according to their probability of producing the peptide map. ProteinInfo ProteinInfo is a collection of tools for retrieval and analysis of protein sequences. The capabilities of the analysis tools include peptide mapping, mass spectrometric fragmentation analysis, disulfide mapping, etc. PeptideMap PeptideMap is a tool for finding modifications on polypeptide sequences. The modifications can be affecting single amino acids (e.g. phoshorylation or oxidation) or cross-linking two amino acids (e.g. disulfide bonds or chemical cross-linking reagents). PepFrag PepFrag is a tool for identifying proteins from a collection of sequences that matches a single tandem mass spectrum. X! Tandem X! Tandem is a tool for identifying proteins from a collection of peptide sequences that matches tandem mass spectra. X! Hunter X! Hunter is a tool for identifying proteins that matches tandem mass spectra to a library of spectra that have been confidently assigned to a particular peptide sequence. GPMDB GPMDB is a database of tandem mass spectra and their assigned peptide sequences. It is designed to aid in the difficult process of validating peptide MS/MS spectra. (A manuscript describing the Global Protein Machine is in press: D. Feny¿, J. Eriksson and R.C. Beavis, "Mass Spectrometric Protein Identification Using the Global Proteome Machine", Methods in Molecular Biology, Computational Biology, Ed. D. Feny¿, Humana Press, Totowa, NJ, in press 2010.) NCDIR Strain Database The National Center for Dynamic Interactome Research (NCDIR) Strain Database

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 我们继续维护基于互联网的蛋白质质谱学生物信息资源。我们还维护用于搜索蛋白质的数据库，并根据用户的要求插入专门的数据库。这些工具可在统一资源定位器http://www.rockefeller.edu/labheads/chait/tools.php上找到，包括： 深刻 EPERVER是一个用多肽质量图搜索蛋白质序列集合的工具。贝叶斯算法被用来根据它们产生肽图的概率来对数据库中的蛋白质序列进行排序。 ProteinInfo ProteinInfo是一组用于检索和分析蛋白质序列的工具。分析工具的功能包括肽图谱、质谱碎片分析、二硫键图谱等。 多肽映射 PeptideMap是一种用于查找多肽序列修饰的工具。修饰可以影响单一氨基酸(例如光短化或氧化)或两个氨基酸的交联性(例如二硫键或化学交联剂)。 PepFrag PepFrag是一种工具，用于从与单个串联质谱图匹配的一组序列中识别蛋白质。 X！串列 X！Tandem是一种工具，用于从与Tandem质谱图匹配的一组肽序列中识别蛋白质。 X！猎人 X！Hunter是一种用于识别蛋白质的工具，该工具将串联质谱库与已被确定为特定多肽的谱库相匹配 序列。 GPMDB GPMDB是串联质谱库及其指定的多肽序列的数据库。它的设计是为了帮助验证多肽MS/MS光谱的困难过程。 (描述全球蛋白质机器的手稿正在印刷中：D.Feny？，J.Eriksson和R.C.Beavis，“使用全球蛋白质组机器的质谱学蛋白质识别”，分子生物学方法，计算生物学，ED。D.Feny？，Humana Press，新泽西州托托瓦，2010年出版。) NCDIR菌株数据库 国家动态相互作用组研究中心(NCDIR)株系数据库