HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries

Research output: Contribution to journalArticlepeer-review


  • Jiarui Zhou
  • Robert Mistrik
  • Zexuan Zhu
  • Zhen Ji
  • Siping Chen

Colleges, School and Institutes

External organisations

  • College of Biomedical Engineering and Instrument Science
  • Zhejiang University
  • College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China.
  • High Chem, Ltd.
  • Shenzhen City Key Laboratory of Embedded System Design
  • College of Computer Science and Software Engineering
  • Shenzhen University


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.

Availability and implementation: Documentation, examples, results and source code are available at http://www.biosciences-labs.bham.ac.uk/viant/hammer/.


Original languageEnglish
Pages (from-to)581-583
Issue number4
Early online date11 Dec 2013
Publication statusPublished - 15 Feb 2014