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

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 experimenta...

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Main Authors:	Zhou, Jiarui, Weber, Ralf J. M., Allwood, J. William, Mistrik, Robert, Zhu, Zexuan, Ji, Zhen, Chen, Siping, Dunn, Warwick B., He, Shan, Viant, Mark R.
Format:	Online
Language:	English
Published:	Oxford University Press 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928522/

id	pubmed-3928522
recordtype	oai_dc
spelling	pubmed-39285222014-02-24 HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries Zhou, Jiarui Weber, Ralf J. M. Allwood, J. William Mistrik, Robert Zhu, Zexuan Ji, Zhen Chen, Siping Dunn, Warwick B. He, Shan Viant, Mark R. Applications Notes 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. Oxford University Press 2014-02-15 2013-12-11 /pmc/articles/PMC3928522/ /pubmed/24336413 http://dx.doi.org/10.1093/bioinformatics/btt711 Text en © The Author 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Zhou, Jiarui Weber, Ralf J. M. Allwood, J. William Mistrik, Robert Zhu, Zexuan Ji, Zhen Chen, Siping Dunn, Warwick B. He, Shan Viant, Mark R.
spellingShingle	Zhou, Jiarui Weber, Ralf J. M. Allwood, J. William Mistrik, Robert Zhu, Zexuan Ji, Zhen Chen, Siping Dunn, Warwick B. He, Shan Viant, Mark R. HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries
author_facet	Zhou, Jiarui Weber, Ralf J. M. Allwood, J. William Mistrik, Robert Zhu, Zexuan Ji, Zhen Chen, Siping Dunn, Warwick B. He, Shan Viant, Mark R.
author_sort	Zhou, Jiarui
title	HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries
title_short	HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries
title_full	HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries
title_fullStr	HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries
title_full_unstemmed	HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries
title_sort	hammer: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries
description	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.
publisher	Oxford University Press
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928522/
_version_	1612059807504662528

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

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