title: HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries.
abstract: CONCLUSIONS
  Experimental MS(n) 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.
  
  
  METHODS
  Documentation, examples, results and source code are available at http://www.biosciences-labs.bham.ac.uk/viant/hammer/.
authors: College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK, HighChem, Ltd., Leskova 11, 81104 Bratislava, Slovakia, Shenzhen City Key Laboratory of Embedded System Design, College of Computer Science and Software Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China and School of Computer Science, University of Birmingham, Birmingham, B15 2TT, UK.
authors: Jiarui
authors: J
authors: Zhou
authors: Ralf J M
authors: RJ
authors: Weber
authors: J William
authors: JW
authors: Allwood
authors: Robert
authors: R
authors: Mistrik
authors: Zexuan
authors: Z
authors: Zhu
authors: Zhen
authors: Z
authors: Ji
authors: Siping
authors: S
authors: Chen
authors: Warwick B
authors: WB
authors: Dunn
authors: Shan
authors: S
authors: He
authors: Mark R
authors: MR
authors: Viant
mesh_terms: D003198:Computer Simulation; D013058:Mass Spectrometry / Q000379:methods*; D055432:Metabolomics; D010363:Pattern Recognition, Automated; D004364:Pharmaceutical Preparations / Q000032:analysis*; D010649:Phenylalanine / Q000378:metabolism*; D012984:Software
chemical_list: D004364:Pharmaceutical Preparations; D010649:Phenylalanine