Introduction

SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: Documentation, examples, results and source code are available at http://www.biosciences-labs.bham.ac.uk/viant/hammer/.

Publications

  1. HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries.
    Cite this
    Zhou J, Weber RJ, Allwood JW, Mistrik R, Zhu Z, Ji Z, Chen S, Dunn WB, He S, Viant MR, 2014-02-01 - Bioinformatics (Oxford, England)

Credits

  1. Jiarui Zhou
    Developer

    College of Biomedical Engineering and Instrument Science, Zhejiang University

  2. Ralf J M Weber
    Developer

  3. J William Allwood
    Developer

  4. Robert Mistrik
    Developer

  5. Zexuan Zhu
    Developer

  6. Zhen Ji
    Developer

  7. Siping Chen
    Developer

  8. Warwick B Dunn
    Developer

  9. Shan He
    Developer

  10. Mark R Viant
    Investigator

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Summary
AccessionBT000109
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByMark R Viant