Metabolomics

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GNPS - Scottish Ale Beer fragmentation data used for substructure mining with MS2LDA

ABSTRACT: This data set was used for the following publication: Topic modeling for untargeted substructure exploration in metabolomics (Van der Hooft et al., 2016, PNAS) (http://www.pnas.org/content/113/48/13738.abstract) Extracts from UK Ales and a German Wheat style beer brewed in Scotland were used to mine for substructures using topic modelling with the newly developed tool MS2LDA. Beer represents a complex mixture of three metabolomes from yeast, hop, and barley, which formed an excellent test case for substructure mining. Data was obtained in positive and in negative ionization mode on a Thermo Scientific Q-Exactive Orbitrap instrument, using stepped collision energy HCD fragmentation in a data-dependent-manner (DDA). The beers used are as follows: Beer 1 Homebrew - German Wheatbeer 6.6% Brewed by Paul Simon Beer 2 Glide Ale 4.6% Jaw Brewery Beer 3 7 Giraffes Extraordinary Ale 5.1% Williams Brewery Beer 4 Black Sheep Ale 4.4% Black Sheep Brewery

INSTRUMENT(S): Q Exactive

ORGANISM(S): Barley Saccharomyces Cerevisiae (ncbitaxon:4932) Humulus Lupulus (ncbitaxon:3486) Ale Beer

SUBMITTER: Justin van der Hooft  

PROVIDER: MSV000081040 | GNPS | Sat Apr 29 10:17:00 BST 2017

REPOSITORIES: GNPS

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Publications

Topic modeling for untargeted substructure exploration in metabolomics.

van der Hooft Justin Johan Jozias JJ   Wandy Joe J   Barrett Michael P MP   Burgess Karl E V KE   Rogers Simon S  

Proceedings of the National Academy of Sciences of the United States of America 20161116 48

The potential of untargeted metabolomics to answer important questions across the life sciences is hindered because of a paucity of computational tools that enable extraction of key biochemically relevant information. Available tools focus on using mass spectrometry fragmentation spectra to identify molecules whose behavior suggests they are relevant to the system under study. Unfortunately, fragmentation spectra cannot identify molecules in isolation but require authentic standards or databases  ...[more]

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