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. 2014 Feb 15;30(4):581-3.
doi: 10.1093/bioinformatics/btt711. Epub 2013 Dec 11.

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

Jiarui Zhou  1 , Ralf J M Weber, J William Allwood, Robert Mistrik, Zexuan Zhu, Zhen Ji, Siping Chen, Warwick B Dunn, Shan He, Mark R Viant
Affiliations

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

Jiarui Zhou et al. Bioinformatics. .

Abstract

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/.

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Figures

Fig. 1.
Fig. 1.
Workflow for HAMMER
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