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主菜单主页产品抗体和抗原牛主机猫主机鸡主机狗主机驴主机山羊主机豚鼠主机仓鼠主机马主机人类主机兔主机大鼠主机杂项主机鼠标主机绵羊主机猪主机实验室设备Biocolor 检测试剂盒细胞分离培养基车关于我们网站地图关于我们隐私政策网上商店条款目录新闻与活动经销商产品搜索Joomla!Accurate Chemical 提供多种驴宿主抗体和抗原到世界各地的测试实验室和研究机构。
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主菜单主页产品抗体和抗原牛宿主猫宿主鸡宿主狗宿主驴宿主山羊宿主豚鼠宿主仓鼠宿主马宿主人类宿主兔子宿主大鼠宿主其他宿主小鼠宿主绵羊宿主猪宿主实验室设备生物彩色检测试剂盒细胞分离培养基车关于我们网站地图关于我们隐私政策网上商店条款目录新闻与活动经销商产品搜索Anal. Chem.All Publications/WebsiteOR SEARCH CITATIONS Recently ViewedYou have not visited any articles yet, Please visit some articles to see contents here. RETURN TO ISSUEPREVArticleNEXTHighly Accurate Chemical Formula Prediction Tool Utilizing High-Resolution Mass Spectra, MS/MS Fragmentation, Heuristic Rules, and Isotope Pattern MatchingTomáš Pluskal*†,Taisuke Uehara‡,andMitsuhiro Yanagida†View Author Information† G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan‡ BioMarkers Personalized Medicine Core Function Unit, Eisai Co., Ltd., Tsukuba, Ibaraki, Japan*E-mail: [email protected]; fax: +81-98-966-2890.Cite this: Anal. Chem. 2012, 84, 10, 4396–4403Publication Date (Web):April 12, 2012Publication History Received11 January 2012Accepted12 April 2012Published online26 April 2012Published inissue 15 May 2012https://doi.org/10.1021/ac3000418Copyright © 2012 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views5868Altmetric-Citations84LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Get e-AlertsAbstractMass spectrometry is commonly applied to qualitatively and quantitatively profile small molecules, such as peptides, metabolites, or lipids. Modern mass spectrometers provide accurate measurements of mass-to-charge ratios of ions, with errors as low as 1 ppm. Even such high mass accuracy, however, is not sufficient to determine the unique chemical formula of each ion, and additional algorithms are necessary. Here we present a universal software tool for predicting chemical formulas from high-resolution mass spectrometry data, developed within the MZmine 2 framework. The tool is based on the use of a combination of heuristic techniques, including MS/MS fragmentation analysis and isotope pattern matching. The performance of the tool was evaluated using a real metabolomic data set obtained with the Orbitrap MS detector. The true formula was correctly determined as the highest-ranking candidate for 79% of the tested compounds. The novel isotope pattern-scoring algorithm outperformed a previously published method in 64% of the tested Orbitrap spectra. The software described in this manuscript is freely available and its source code can be accessed within the MZmine 2 source code repository.Supporting InformationARTICLE SECTIONSJump ToTable S1: Parameter settings used for data processing with MZmine 2.7.2. Table S2: Formal valence of elements for the calculation of RDBE values. Table S3: Parameters used to perform the chemical formula prediction. Table S4: Results of the formula prediction evaluation. Table S5: Results of the comparison of the isotope pattern-scoring algorithms of MZmine 2 and SIRIUS. Figure S6: Detected and predicted isotope patterns of acetyl-CoA. Additionally, the raw data file used for the evaluation in mzXML format,(19) the MZmine 2 project file, the SIRIUS workspace file, and the lists of all the generated chemical formulas used for evaluation. This material is available free of charge via the Internet at http://pubs.acs.org.ac3000418_si_001.zip (24.12 MB) Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html. Cited ByThis article is cited by 84 publications.Kevin J. Murray, Erik S. Carlson, Alessia Stornetta, Emily P. Balskus, Peter W. Villalta, Silvia Balbo. Extension of Diagnostic Fragmentation Filtering for Automated Discovery in DNA Adductomics. 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Planta 2019, 250 , 857-871. https://doi.org/10.1007/s00425-019-03211-5Junjie Hu, Fei Liu, Nan Feng, Huangxian Ju. Selenium-isotopic signature toward mass spectrometric identification and enzyme activity assay. Analytica Chimica Acta 2019, 1064 , 1-10. https://doi.org/10.1016/j.aca.2019.03.045María Eugenia Monge, James N. Dodds, Erin S. Baker, Arthur S. Edison, Facundo M. Fernández. Challenges in Identifying the Dark Molecules of Life. Annual Review of Analytical Chemistry 2019, 12 , 177-199. https://doi.org/10.1146/annurev-anchem-061318-114959Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Alexander A. Aksenov, Alexey V. Melnik, Marvin Meusel, Pieter C. Dorrestein, Juho Rousu, Sebastian Böcker. SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information. Nature Methods 2019, 16 , 299-302. https://doi.org/10.1038/s41592-019-0344-8Martin Brüggemann, Dominik van Pinxteren, Yuchen Wang, Jian Zhen Yu, Hartmut Herrmann. 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Metabolomic Analysis of Schizosaccharomyces pombe : Sample Preparation, Detection, and Data Interpretation. Cold Spring Harbor Protocols 2016, 2016 (12) , pdb.top079921. https://doi.org/10.1101/pdb.top079921Sebastian Böcker, Kai Dührkop. Fragmentation trees reloaded. Journal of Cheminformatics 2016, 8 https://doi.org/10.1186/s13321-016-0116-8Hendrik Treutler, Steffen Neumann. Prediction, Detection, and Validation of Isotope Clusters in Mass Spectrometry Data. Metabolites 2016, 6 , 37. https://doi.org/10.3390/metabo6040037Lieven Van Meulebroek, Jochen Hanssens, Kathy Steppe, Lynn Vanhaecke. Metabolic Fingerprinting to Assess the Impact of Salinity on Carotenoid Content in Developing Tomato Fruits. International Journal of Molecular Sciences 2016, 17 , 821. https://doi.org/10.3390/ijms17060821Mingjing Zhang, Zhimin Zhang, Chen Chen, Hongmei Lu, Yizeng Liang. Parallel formula generator based on branch-and-bound algorithm for elucidating high resolution mass spectra. 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Journal of Chromatography A 2012, 1259 , 3-15. https://doi.org/10.1016/j.chroma.2012.08.072 Export articles to Mendeley Get article recommendations from ACS based on references in your Mendeley library. Export articles to Mendeley Get article recommendations from ACS based on references in your Mendeley library. Please note: If you switch to a different device, you may be asked to login again with only your ACS ID. Please note: If you switch to a different device, you may be asked to login again with only your ACS ID. Please note: If you switch to a different device, you may be asked to login again with only your ACS ID. Please login with your ACS ID before connecting to your Mendeley account.Login with ACS ID This website uses cookies to improve your user experience. By continuing to use the site, you are accepting our use of cookies. Read the ACS privacy policy. CONTINUE