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

Zhou J, Weber RJ, Allwood JW, Mistrik R, Zhu Z, Ji Z, Chen S, Dunn WB, He S, Viant MR - Bioinformatics (2013)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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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Related in: MedlinePlus

Workflow for HAMMER
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btt711-F1: Workflow for HAMMER

Mentions: As shown in Figure 1, HAMMER consists of four modules:


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

Zhou J, Weber RJ, Allwood JW, Mistrik R, Zhu Z, Ji Z, Chen S, Dunn WB, He S, Viant MR - Bioinformatics (2013)

Workflow for HAMMER
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3928522&req=5

btt711-F1: Workflow for HAMMER
Mentions: As shown in Figure 1, HAMMER consists of four modules:

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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/.

Show MeSH
Related in: MedlinePlus