{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,25]],"date-time":"2025-10-25T14:14:23Z","timestamp":1761401663037},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1026,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Experimental MSn mass spectral libraries currently do not adequately cover chemical space. This limits the robust annotation of metabolites in metabolomics studies of complex biological samples. In silico fragmentation libraries would improve the identification of compounds from experimental multistage fragmentation data when experimental reference data are unavailable. Here, we present a freely available software package to automatically control Mass Frontier software to construct in silico mass spectral libraries and to perform spectral matching. Based on two case studies, we have demonstrated that high-throughput automation of Mass Frontier allows researchers to generate in silico mass spectral libraries in an automated and high-throughput fashion with little or no human intervention required.<\/jats:p>\n               <jats:p>Availability and implementation: Documentation, examples, results and source code are available at http:\/\/www.biosciences-labs.bham.ac.uk\/viant\/hammer\/.<\/jats:p>\n               <jats:p>Contact: \u00a0m.viant@bham.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt711","type":"journal-article","created":{"date-parts":[[2013,12,13]],"date-time":"2013-12-13T02:10:14Z","timestamp":1386900614000},"page":"581-583","source":"Crossref","is-referenced-by-count":38,"title":["HAMMER: automated operation of mass frontier to construct <i>in silico<\/i> mass spectral fragmentation libraries"],"prefix":"10.1093","volume":"30","author":[{"given":"Jiarui","family":"Zhou","sequence":"first","affiliation":[{"name":"1 College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China, 2School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK, 3HighChem, Ltd., Leskova 11, 81104 Bratislava, Slovakia, 4Shenzhen City Key Laboratory of Embedded System Design, College of Computer Science and Software Engineering, 5School of Medicine, Shenzhen University, Shenzhen 518060, China and 6School of Computer Science, University of Birmingham, Birmingham, B15 2TT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ralf J. M.","family":"Weber","sequence":"additional","affiliation":[{"name":"1 College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China, 2School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK, 3HighChem, Ltd., Leskova 11, 81104 Bratislava, Slovakia, 4Shenzhen City Key Laboratory of Embedded System Design, College of Computer Science and Software Engineering, 5School of Medicine, Shenzhen University, Shenzhen 518060, China and 6School of Computer Science, University of Birmingham, Birmingham, B15 2TT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J. William","family":"Allwood","sequence":"additional","affiliation":[{"name":"1 College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China, 2School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK, 3HighChem, Ltd., Leskova 11, 81104 Bratislava, Slovakia, 4Shenzhen City Key Laboratory of Embedded System Design, College of Computer Science and Software Engineering, 5School of Medicine, Shenzhen University, Shenzhen 518060, China and 6School of Computer Science, University of Birmingham, Birmingham, B15 2TT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Mistrik","sequence":"additional","affiliation":[{"name":"1 College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China, 2School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK, 3HighChem, Ltd., Leskova 11, 81104 Bratislava, Slovakia, 4Shenzhen City Key Laboratory of Embedded System Design, College of Computer Science and Software Engineering, 5School of Medicine, Shenzhen University, Shenzhen 518060, China and 6School of Computer Science, University of Birmingham, Birmingham, B15 2TT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zexuan","family":"Zhu","sequence":"additional","affiliation":[{"name":"1 College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China, 2School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK, 3HighChem, Ltd., Leskova 11, 81104 Bratislava, Slovakia, 4Shenzhen City Key Laboratory of Embedded System Design, College of Computer Science and Software Engineering, 5School of Medicine, Shenzhen University, Shenzhen 518060, China and 6School of Computer Science, University of Birmingham, Birmingham, B15 2TT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhen","family":"Ji","sequence":"additional","affiliation":[{"name":"1 College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China, 2School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK, 3HighChem, Ltd., Leskova 11, 81104 Bratislava, Slovakia, 4Shenzhen City Key Laboratory of Embedded System Design, College of Computer Science and Software Engineering, 5School of Medicine, Shenzhen University, Shenzhen 518060, China and 6School of Computer Science, University of Birmingham, Birmingham, B15 2TT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siping","family":"Chen","sequence":"additional","affiliation":[{"name":"1 College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China, 2School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK, 3HighChem, Ltd., Leskova 11, 81104 Bratislava, Slovakia, 4Shenzhen City Key Laboratory of Embedded System Design, College of Computer Science and Software Engineering, 5School of Medicine, Shenzhen University, Shenzhen 518060, China and 6School of Computer Science, University of Birmingham, Birmingham, B15 2TT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Warwick B.","family":"Dunn","sequence":"additional","affiliation":[{"name":"1 College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China, 2School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK, 3HighChem, Ltd., Leskova 11, 81104 Bratislava, Slovakia, 4Shenzhen City Key Laboratory of Embedded System Design, College of Computer Science and Software Engineering, 5School of Medicine, Shenzhen University, Shenzhen 518060, China and 6School of Computer Science, University of Birmingham, Birmingham, B15 2TT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shan","family":"He","sequence":"additional","affiliation":[{"name":"1 College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China, 2School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK, 3HighChem, Ltd., Leskova 11, 81104 Bratislava, Slovakia, 4Shenzhen City Key Laboratory of Embedded System Design, College of Computer Science and Software Engineering, 5School of Medicine, Shenzhen University, Shenzhen 518060, China and 6School of Computer Science, University of Birmingham, Birmingham, B15 2TT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark R.","family":"Viant","sequence":"additional","affiliation":[{"name":"1 College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China, 2School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK, 3HighChem, Ltd., Leskova 11, 81104 Bratislava, Slovakia, 4Shenzhen City Key Laboratory of Embedded System Design, College of Computer Science and Software Engineering, 5School of Medicine, Shenzhen University, Shenzhen 518060, China and 6School of Computer Science, University of Birmingham, 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