MetaboSearch: Tool for Mass-Based Metabolite Identification Using Multiple Databases
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{"title"=>"Metabosearch: Tool for mass-based metabolite identification using multiple databases", "type"=>"journal", "authors"=>[{"first_name"=>"Bin", "last_name"=>"Zhou", "scopus_author_id"=>"18938013300"}, {"first_name"=>"Jinlian", "last_name"=>"Wang", "scopus_author_id"=>"35243754800"}, {"first_name"=>"Habtom W.", "last_name"=>"Ressom", "scopus_author_id"=>"6603922272"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"22768229", "doi"=>"10.1371/journal.pone.0040096", "sgr"=>"84863084745", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "scopus"=>"2-s2.0-84863084745", "issn"=>"19326203", "pui"=>"365133274"}, "id"=>"26d4f0e6-d65e-39a7-8fb1-9e2b523acaa5", "abstract"=>"UNLABELLED: 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.\\n\\nAVAILABILITY: The software tool is available at http://omics.georgetown.edu/MetaboSearch.html.", "link"=>"http://www.mendeley.com/research/metabosearch-tool-massbased-metabolite-identification-using-multiple-databases", "reader_count"=>89, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Student > Doctoral Student"=>5, "Researcher"=>35, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>4, "Student > Master"=>8, "Other"=>3, "Student > Bachelor"=>3, "Lecturer"=>2, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Student > Doctoral Student"=>5, "Researcher"=>35, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>4, "Student > Master"=>8, "Other"=>3, "Student > Bachelor"=>3, "Lecturer"=>2, "Professor"=>3}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Unspecified"=>4, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>8, "Mathematics"=>3, "Medicine and Dentistry"=>7, "Agricultural and Biological Sciences"=>36, "Physics and Astronomy"=>1, "Chemistry"=>20, "Computer Science"=>4, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>7}, "Chemistry"=>{"Chemistry"=>20}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>36}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Mathematics"=>{"Mathematics"=>3}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Netherlands"=>1, "Belgium"=>1, "United States"=>2, "Brazil"=>1, "United Kingdom"=>1, "South Africa"=>1, "Switzerland"=>1, "Germany"=>1, "India"=>1}, "group_count"=>3}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/616137"], "description"=>"<p>The figures in parenthesis indicate the number of m/z values with at least one putative identification.</p>", "links"=>[], "tags"=>["putative", "identifications", "acquired", "databases", "compared"], "article_id"=>286630, "categories"=>["Biochemistry", "Biological Sciences", "Chemistry", "Information And Computing Sciences"], "users"=>["Bin Zhou", "Jinlian Wang", "Habtom W. Ressom"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040096.t001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_number_of_putative_identifications_acquired_by_each_of_the_four_databases_compared_to_MetaboSearch_/286630", "title"=>"The number of putative identifications acquired by each of the four databases compared to MetaboSearch.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 03:10:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/615870"], "description"=>"<p>The software architecture of MetaboSearch.</p>", "links"=>[], "tags"=>["chemistry", "Computational biology", "computer science", "Biochemistry"], "article_id"=>286358, "categories"=>["Biochemistry", "Biological Sciences", "Chemistry", "Information And Computing Sciences"], "users"=>["Bin Zhou", "Jinlian Wang", "Habtom W. Ressom"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040096.g002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_software_architecture_of_MetaboSearch_/286358", "title"=>"The software architecture of MetaboSearch.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 03:08:31"}

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