{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,26]],"date-time":"2024-08-26T13:06:02Z","timestamp":1724677562753},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Metabolome analysis with GC\/MS has meanwhile been established as one of the \"omics\" techniques. Compound identification is done by comparison of the MS data with compound libraries. Mass spectral libraries in the field of metabolomics ought to connect the relevant mass traces of the metabolites to other relevant data, e.g. formulas, chemical structures, identification numbers to other databases etc. Since existing solutions are either commercial and therefore only available for certain instruments or not capable of storing such information, there is need to provide a software tool for the management of such data.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here we present mSpecs, an open source software tool to manage mass spectral data in the field of metabolomics. It provides editing of mass spectra and virtually any associated information, automatic calculation of formulas and masses and is extensible by scripts. The graphical user interface is capable of common techniques such as copy\/paste, undo\/redo and drag and drop. It owns import and export filters for the major public file formats in order to provide compatibility to commercial instruments.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>mSpecs is a versatile tool for the management and editing of mass spectral libraries in the field of metabolomics. Beyond that it provides capabilities for the automatic management of libraries though its scripting functionality. mSpecs can be used on all major platforms and is licensed under the GNU General Public License and available at<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/mspecs.tu-bs.de\" ext-link-type=\"uri\">http:\/\/mspecs.tu-bs.de<\/jats:ext-link>.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-10-229","type":"journal-article","created":{"date-parts":[[2009,8,21]],"date-time":"2009-08-21T18:13:40Z","timestamp":1250878420000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["mSpecs: a software tool for the administration and editing of mass spectral libraries in the field of metabolomics"],"prefix":"10.1186","volume":"10","author":[{"given":"Bernhard","family":"Thielen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephanie","family":"Heinen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dietmar","family":"Schomburg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,7,22]]},"reference":[{"key":"2959_CR1","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1023\/A:1013713905833","volume":"48","author":"O Fiehn","year":"2002","unstructured":"Fiehn O: Metabolomics \u2013 the link between genotypes and phenotypes. Plant Molecular Biology 2002, 48: 155\u2013171. 10.1023\/A:1013713905833","journal-title":"Plant Molecular Biology"},{"key":"2959_CR2","doi-asserted-by":"publisher","first-page":"669","DOI":"10.1146\/annurev.arplant.54.031902.135014","volume":"54","author":"W Weckwerth","year":"2003","unstructured":"Weckwerth W: Metabolomics in systems biology. Annual Review of Plant Biology 2003, 54: 669\u2013689. 10.1146\/annurev.arplant.54.031902.135014","journal-title":"Annual Review of Plant Biology"},{"key":"2959_CR3","doi-asserted-by":"publisher","first-page":"1142","DOI":"10.1038\/81116","volume":"18","author":"N Glassbrook","year":"2000","unstructured":"Glassbrook N, Beecher C, Ryals J: Metabolic profiling on the right path. Nature Biotechnology 2000, 18: 1142\u20131143. 10.1038\/81116","journal-title":"Nature Biotechnology"},{"key":"2959_CR4","doi-asserted-by":"publisher","first-page":"s109","DOI":"10.1186\/gb-2004-5-6-109","volume":"5","author":"J Kopka","year":"2004","unstructured":"Kopka J, Fernie A, Weckwerth W, Gibon Y, Stitt M: Metabolite profiling in plant biology: platforms and destinations. Genome Biology 2004, 5: s109. 10.1186\/gb-2004-5-6-109","journal-title":"Genome Biology"},{"key":"2959_CR5","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1016\/j.mib.2004.04.012","volume":"7","author":"DB Kell","year":"2004","unstructured":"Kell DB: Metabolomics and systems biology: making sense of the soup. Current Opinion in Microbiology 2004, 7: 296\u2013307. 10.1016\/j.mib.2004.04.012","journal-title":"Current Opinion in Microbiology"},{"key":"2959_CR6","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1093\/jxb\/eri010","volume":"56","author":"P Krishnan","year":"2005","unstructured":"Krishnan P, Kruger NJ, Ratcliffe RG: Metabolite fingerprinting and profiling in plants using NMR. Journal of Experimental Botany 2005, 56: 255\u2013265. 10.1093\/jxb\/eri010","journal-title":"Journal of Experimental Botany"},{"key":"2959_CR7","doi-asserted-by":"publisher","first-page":"606","DOI":"10.1039\/b418288j","volume":"130","author":"WB Dunn","year":"2005","unstructured":"Dunn WB, Bailey NJ, Johnson HE: Measuring the metabolome: current analytical technologies. The Analyst 2005, 130: 606\u2013625. 10.1039\/b418288j","journal-title":"The Analyst"},{"key":"2959_CR8","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1515\/BC.2004.111","volume":"385","author":"S Strelkov","year":"2004","unstructured":"Strelkov S, von Elstermann M, Schomburg D: Comprehensive analysis of metabolites in Corynebacterium glutamicum by gas chromatography\/mass spectrometry. Biological Chemistry 2004, 385: 853\u2013861. 10.1515\/BC.2004.111","journal-title":"Biological Chemistry"},{"key":"2959_CR9","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1093\/jxb\/eri069","volume":"56","author":"JM Halket","year":"2005","unstructured":"Halket JM, Waterman D, Przyborowska AM, Raj PKP, Fraser PD, Bramley PM: Chemical derivatization and mass spectral libraries in metabolic profiling by GC\/MS and LC\/MS\/MS. Journal of Experimental Botany 2005, 56: 219\u2013243. 10.1093\/jxb\/eri069","journal-title":"Journal of Experimental Botany"},{"key":"2959_CR10","doi-asserted-by":"publisher","first-page":"1915","DOI":"10.1002\/hlca.19580410703","volume":"41","author":"E Kov\u00e1ts","year":"1958","unstructured":"Kov\u00e1ts E: Gas-chromatographische Charakteriserung organischer Verbindungen.Teil 1: Retentionsindices aliphatischer Halogenide, Alkohole, Aldehyde und Ketone. Helvetica Chimica Acta 1958, 41: 1915\u20131932. 10.1002\/hlca.19580410703","journal-title":"Helvetica Chimica Acta"},{"key":"2959_CR11","doi-asserted-by":"publisher","first-page":"s109","DOI":"10.1186\/1471-2105-7-109","volume":"7","author":"BH Junker","year":"2006","unstructured":"Junker BH, Klukas C, Schreiber F: VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 2006, 7: s109. 10.1186\/1471-2105-7-109","journal-title":"BMC Bioinformatics"},{"key":"2959_CR12","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 2003, 13: 2498\u20132504. 10.1101\/gr.1239303","journal-title":"Genome Research"},{"key":"2959_CR13","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1093\/nar\/27.1.29","volume":"27","author":"H Ogata","year":"1999","unstructured":"Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 1999, 27: 29\u201334. 10.1093\/nar\/27.1.29","journal-title":"Nucleic Acids Research"},{"key":"2959_CR14","unstructured":"National Institute of Standards and Technology: NIST Standard Reference Database 1A.[http:\/\/www.nist.gov\/data\/nist1a.htm]"},{"key":"2959_CR15","unstructured":"Stein SE, Mallard G: AMDIS.[http:\/\/chemdata.nist.gov\/mass-spc\/amdis\/]"},{"key":"2959_CR16","first-page":"U1025","volume":"230","author":"S Heller","year":"2005","unstructured":"Heller S, Stein S, Tchekhovskoi D: InChI: Open access\/open source and the IUPAC international chemical identifier. Abstracts of the Papers of the American Chemical Society 2005, 230: U1025-U1026.","journal-title":"Abstracts of the Papers of the American Chemical Society"},{"key":"2959_CR17","unstructured":"GNU Operating System: GNU General Public License.[http:\/\/www.gnu.org\/licenses\/gpl.html]"},{"key":"2959_CR18","unstructured":"Nokia: Qt \u2013 A cross-platform application and UI framework.[http:\/\/www.qtsoftware.com\/]"},{"key":"2959_CR19","unstructured":"ChemZoo: Chemspider.[http:\/\/www.chemspider.com\/]"},{"key":"2959_CR20","doi-asserted-by":"publisher","first-page":"D521","DOI":"10.1093\/nar\/gkl923","volume":"35","author":"DS Wishart","year":"2007","unstructured":"Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly M, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, Macinnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L: HMDB: the Human Metabolome Database. Nucleic Acids Research 2007, 35: D521-D526. 10.1093\/nar\/gkl923","journal-title":"Nucleic Acids Research"},{"key":"2959_CR21","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1021\/ci00057a005","volume":"28","author":"D Weininger","year":"1988","unstructured":"Weininger D: SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. Journal of Chemical Information and Computer Sciences 1988, 28: 31\u201336.","journal-title":"Journal of Chemical Information and Computer Sciences"},{"key":"2959_CR22","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1021\/ac00253a037","volume":"55","author":"J Yergey","year":"1983","unstructured":"Yergey J, Heller D, Hansen G, Cotter RJ, Fenselau C: Isotopic Distributions in Mass Spectra of Large Molecules. Analytical Chemistry 1983, 55: 353\u2013356. 10.1021\/ac00253a037","journal-title":"Analytical Chemistry"},{"key":"2959_CR23","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1021\/ci00007a012","volume":"32","author":"A Dalby","year":"1992","unstructured":"Dalby A, Nourse JG, Hounshell DW, Gushurst AK, Grier DL, Leland BA, Laufer J: Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited. Journal of Chemical Information and Computer Sciences 1992, 32: 244\u2013255.","journal-title":"Journal of Chemical Information and Computer Sciences"},{"key":"2959_CR24","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1039\/cs9972600001","volume":"26","author":"P Murray-Rust","year":"1997","unstructured":"Murray-Rust P, Rzepa HS, Whitaker BJ: The World-Wide Web as a chemical information tool. Chemical Society Reviews 1997, 26: 1\u201310. 10.1039\/cs9972600001","journal-title":"Chemical Society Reviews"},{"key":"2959_CR25","unstructured":"World Wide Web Consortium: Scalable vector graphics.[http:\/\/www.w3.org\/Graphics\/SVG\/]"},{"key":"2959_CR26","unstructured":"Thermo Sceintific: Xcalibur.[http:\/\/www.thermo.com\/com\/cda\/product\/detail\/0,1055,1000001009250,00.html]"},{"key":"2959_CR27","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1366\/0003702944027840","volume":"48","author":"P Lampen","year":"1994","unstructured":"Lampen P, Hillig H, Davies AN, Linscheid M: JCAMP-DX for Mass Spectrometry. Applied Spectroscopy 1994, 48: 1545\u20131552.","journal-title":"Applied Spectroscopy"},{"key":"2959_CR28","unstructured":"Agilent Technologies: Chemstation.[http:\/\/www.chem.agilent.com\/scripts\/pds.asp?lpage=282]"},{"key":"2959_CR29","unstructured":"Adobe: Adobe PDF Technology Center.[http:\/\/www.adobe.com\/devnet\/pdf\/pdf_reference.html]"},{"key":"2959_CR30","unstructured":"World Wide Web Consortium: Extensible Markup Language (XML).[http:\/\/www.w3.org\/XML\/]"},{"key":"2959_CR31","unstructured":"ECMA International: Standard ECMA-262.[http:\/\/www.ecma-international.org\/publications\/standards\/Ecma-262.htm]"},{"key":"2959_CR32","doi-asserted-by":"publisher","first-page":"2962","DOI":"10.1093\/bioinformatics\/btl526","volume":"22","author":"B Bunk","year":"2006","unstructured":"Bunk B, Kucklick M, Jonas R, M\u00fcnch R, Schobert M, Jahn D, Hiller K: MetaQuant: a tool for the automatic quantification of GC\/MS-based metabolome data. Bioinformatics 2006, 22: 2962\u20132965. 10.1093\/bioinformatics\/btl526","journal-title":"Bioinformatics"},{"key":"2959_CR33","doi-asserted-by":"publisher","first-page":"s59","DOI":"10.1186\/1471-2105-8-59","volume":"8","author":"O Spjuth","year":"2007","unstructured":"Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J, Murray-Rust P, Steinbeck C, Wikberg JES: Bioclipse: an open source workbench for chemo- and bioinformatics. BMC Bioinformatics 2007, 8: s59. 10.1186\/1471-2105-8-59","journal-title":"BMC Bioinformatics"},{"key":"2959_CR34","doi-asserted-by":"publisher","first-page":"770","DOI":"10.1016\/S1044-0305(99)00047-1","volume":"10","author":"SE Stein","year":"1999","unstructured":"Stein SE: An Integrated Method for Spectrum Extraction and Compound Identification from Gas Chromatography\/Mass Spectrometry Data. Journal of the American Society of Mass Spectrometry 1999, 10: 770\u2013781. 10.1016\/S1044-0305(99)00047-1","journal-title":"Journal of the American Society of Mass Spectrometry"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-229.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,26]],"date-time":"2023-05-26T12:08:19Z","timestamp":1685102899000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-229"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,7,22]]},"references-count":34,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["2959"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-229","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,7,22]]},"assertion":[{"value":"19 September 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 July 2009","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 July 2009","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"229"}}