MetaboSearch: tool for mass-based metabolite identification using multiple databases.
MetaboSearch: tool for mass-based metabolite identification using multiple databases.
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DOI：
10.1371/journal.pone.0040096
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Ressom HW
中科院分区：
文献类型：
--
作者：
Zhou B;Wang J;Ressom HW
根据代谢物的质量在数据库中搜索代谢物通常是基于质谱学的非靶向代谢组学研究的代谢物鉴定的第一步。主要的代谢物数据库包括人类代谢组数据库(HMDB)、麦迪逊代谢组学联盟数据库(MMCD)、Metlin和血脂图谱。由于这些数据库中的每一个只涵盖代谢组的一小部分，因此整合这些数据库的搜索结果有望产生更全面的覆盖。然而，当需要识别数百种代谢物时，手动组合多个搜索结果通常是困难的。我们已经实施了一个基于网络的软件工具，可以同时对四个主要数据库进行大规模搜索，并整合结果。此外，通过交叉参考多个数据库来检索更完整的代谢物的化学标识信息。根据IUPAC国际化学识别符(INCHI)关键字合并搜索结果。除了简单的m/z值列表外，该软件还可以接受离子注释信息作为增强代谢物识别的输入。在正负电离模式下获得的质谱图数据上验证了该软件的性能。与单个数据库的搜索结果相比，MetbraSearch提供了更好的代谢组覆盖范围和更完整的化学识别信息。可用性：该软件工具可在http://omics.georgetown.edu/MetaboSearch.html.上获得
Searching metabolites against databases according to their masses is often the first step in metabolite identification for a mass spectrometry-based untargeted metabolomics study. Major metabolite databases include Human Metabolome DataBase (HMDB), Madison Metabolomics Consortium Database (MMCD), Metlin, and LIPID MAPS. Since each one of these databases covers only a fraction of the metabolome, integration of the search results from these databases is expected to yield a more comprehensive coverage. However, the manual combination of multiple search results is generally difficult when identification of hundreds of metabolites is desired. We have implemented a web-based software tool that enables simultaneous mass-based search against the four major databases, and the integration of the results. In addition, more complete chemical identifier information for the metabolites is retrieved by cross-referencing multiple databases. The search results are merged based on IUPAC International Chemical Identifier (InChI) keys. Besides a simple list of m/z values, the software can accept the ion annotation information as input for enhanced metabolite identification. The performance of the software is demonstrated on mass spectrometry data acquired in both positive and negative ionization modes. Compared with search results from individual databases, MetaboSearch provides better coverage of the metabolome and more complete chemical identifier information. Availability: The software tool is available at http://omics.georgetown.edu/MetaboSearch.html.
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影响因子：
14.9
作者：
Wishart DS;Knox C;Guo AC;Eisner R;Young N;Gautam B;Hau DD;Psychogios N;Dong E;Bouatra S;Mandal R;Sinelnikov I;Xia J;Jia L;Cruz JA;Lim E;Sobsey CA;Shrivastava S;Huang P;Liu P;Fang L;Peng J;Fradette R;Cheng D;Tzur D;Clements M;Lewis A;De Souza A;Zuniga A;Dawe M;Xiong Y;Clive D;Greiner R;Nazyrova A;Shaykhutdinov R;Li L;Vogel HJ;Forsythe I
通讯作者：
Forsythe I
DOI：
10.1093/bioinformatics/btq476
发表时间：
2010-10-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Wohlgemuth G;Haldiya PK;Willighagen E;Kind T;Fiehn O
通讯作者：
Fiehn O
影响因子：
2.5
作者：
Smith, CA;O'Maille, G;Siuzdak, G
通讯作者：
Siuzdak, G
影响因子：
14.9
作者：
Sud M;Fahy E;Cotter D;Brown A;Dennis EA;Glass CK;Merrill AH Jr;Murphy RC;Raetz CR;Russell DW;Subramaniam S
通讯作者：
Subramaniam S
影响因子：
1.8
作者：
Scheltema, R. A.;Decuypere, S.;Breitling, R.
通讯作者：
Breitling, R.