Dataset Information

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

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/.

SUBMITTER: Zhou J

PROVIDER: S-EPMC3928522 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature

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Publications

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

Zhou Jiarui J Weber Ralf J M RJ Allwood J William JW Mistrik Robert R Zhu Zexuan Z Ji Zhen Z Chen Siping S Dunn Warwick B WB He Shan S Viant Mark R MR

Bioinformatics (Oxford, England) 20131211 4

<h4>Summary</h4>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 const ...[more]

PMID: 24336413

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Project description:BackgroundMass spectrometry has become the analytical method of choice in metabolomics research. The identification of unknown compounds is the main bottleneck. In addition to the precursor mass, tandem MS spectra carry informative fragment peaks, but the coverage of spectral libraries of measured reference compounds are far from covering the complete chemical space. Compound libraries such as PubChem or KEGG describe a larger number of compounds, which can be used to compare their in silico fragmentation with spectra of unknown metabolites.ResultsWe created the MetFrag suite to obtain a candidate list from compound libraries based on the precursor mass, subsequently ranked by the agreement between measured and in silico fragments. In the evaluation MetFrag was able to rank most of the correct compounds within the top 3 candidates returned by an exact mass query in KEGG. Compared to a previously published study, MetFrag obtained better results than the commercial MassFrontier software. Especially for large compound libraries, the candidates with a good score show a high structural similarity or just different stereochemistry, a subsequent clustering based on chemical distances reduces this redundancy. The in silico fragmentation requires less than a second to process a molecule, and MetFrag performs a search in KEGG or PubChem on average within 30 to 300 seconds, respectively, on an average desktop PC.ConclusionsWe presented a method that is able to identify small molecules from tandem MS measurements, even without spectral reference data or a large set of fragmentation rules. With today's massive general purpose compound libraries we obtain dozens of very similar candidates, which still allows a confident estimate of the correct compound class. Our tool MetFrag improves the identification of unknown substances from tandem MS spectra and delivers better results than comparable commercial software. MetFrag is available through a web application, web services and as java library. The web frontend allows the end-user to analyse single spectra and browse the results, whereas the web service and console application are aimed to perform batch searches and evaluation.

Dataset Information

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

Summary

Availability and implementation

Publications

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

Similar Datasets

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