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: 8169103
• 负责人: JULIO C PADOVAN
• 金额: $ 0.93万
• 依托单位: ROCKEFELLER UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-03-01 至 2011-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8169103
• 关键词: Affect; Algorithms; Amino Acid Sequence; Amino Acids; Bioinformatics; Chemicals; Collection; Computational Biology; Computer Retrieval of Information on Scientific Projects Database; Cross-Linking Reagents; Databases; Disulfides; Funding; Grant; Institution; Internet; Libraries; Manuscripts; Maps; Mass Spectrum Analysis; Methods; Modification; Molecular Biology; Peptide Mapping; Peptide Sequence Determination; Peptides; Probability; Process; Protein Sequence Analysis; Proteins; Proteome; Research; Research Personnel; Resources; Retrieval; Source; United States National Institutes of Health; base; crosslink; design; disulfide bond; 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. 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. We continue to maintain an internet based bioinformatic resource for protein mass spectrometry. 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 Macine 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

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以出现在其他 CRISP 条目中 列出的机构是。 对于中心来说，它不一定是研究者的机构。 我们继续维护基于互联网的蛋白质质谱生物信息资源，这些工具可以在通用资源定位器 http://www.rockefeller.edu/labheads/chait/tools.php 上找到，包括： 深刻的 ProFound 是一种通过肽质量图搜索蛋白质序列集合的工具，使用贝叶斯算法根据生成肽图的概率对数据库中的蛋白质序列进行排序。 蛋白质信息 ProteinInfo是蛋白质序列检索和分析的工具集合，分析工具的功能包括肽图谱、质谱碎片分析、二硫键图谱等。 肽图 PeptideMap 是一种用于查找多肽序列修饰的工具，这些修饰可以影响单个氨基酸（例如磷酸化或氧化）或交联两个氨基酸（例如二硫键或化学交联试剂）。 佩普弗拉格 PepFrag 是一种从与单个串联质谱相匹配的序列集合中识别蛋白质的工具。 串联！ X! Tandem 是一种从与串联质谱相匹配的肽序列集合中识别蛋白质的工具。 猎人！ X! Hunter 是一种用于识别蛋白质的工具，该工具将串联质谱与已自信地分配给特定肽的光谱库相匹配 顺序。 通用数据库 GPMDB 是串联质谱及其指定肽序列的数据库，旨在帮助完成验证肽 MS/MS 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进行质谱蛋白质鉴定”，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) 菌株数据库