Show simple item record

dc.contributor.author John en_US
dc.contributor.author David Pierre Louis en_US
dc.contributor.author David A en_US
dc.contributor.author Manfred en_US
dc.contributor.author Stuart en_US
dc.contributor.author Wanchang en_US
dc.contributor.author Hassan en_US
dc.date.accessioned 2010-03-17T11:33:47Z
dc.date.available 2010-03-17T11:33:47Z
dc.date.issued 2009-07-21 en_US
dc.identifier http://dx.doi.org/10.1186/1471-2105-10-227 en_US
dc.identifier.citation Draper , J , Enot , D P L , Parker , D A , Beckmann , M , Snowdon , S , Lin , W & Zubair , H 2009 , ' Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules' ' BMC Bioinformatics , vol 10 , no. 227 , 227 . , 10.1186/1471-2105-10-227 en_US
dc.identifier.other PURE: 145507 en_US
dc.identifier.other dspace: 2160/4464 en_US
dc.identifier.uri http://hdl.handle.net/2160/4464
dc.description.abstract Background Metabolomics experiments using Mass Spectrometry (MS) technology measure the mass to charge ratio (m/z) and intensity of ionised molecules in crude extracts of complex biological samples to generate high dimensional metabolite 'fingerprint' or metabolite 'profile' data. High resolution MS instruments perform routinely with a mass accuracy of <5 ppm (parts per million) thus providing potentially a direct method for signal putative annotation using databases containing metabolite mass information. Most database interfaces support only simple queries with the default assumption that molecules either gain or lose a single proton when ionised. In reality the annotation process is confounded by the fact that many ionisation products will be not only molecular isotopes but also salt/solvent adducts and neutral loss fragments of original metabolites. This report describes an annotation strategy that will allow searching based on all potential ionisation products predicted to form during electrospray ionisation (ESI). Results Metabolite 'structures' harvested from publicly accessible databases were converted into a common format to generate a comprehensive archive in MZedDB. 'Rules' were derived from chemical information that allowed MZedDB to generate a list of adducts and neutral loss fragments putatively able to form for each structure and calculate, on the fly, the exact molecular weight of every potential ionisation product to provide targets for annotation searches based on accurate mass. We demonstrate that data matrices representing populations of ionisation products generated from different biological matrices contain a large proportion (sometimes > 50%) of molecular isotopes, salt adducts and neutral loss fragments. Correlation analysis of ESI-MS data features confirmed the predicted relationships of m/z signals. An integrated isotope enumerator in MZedDB allowed verification of exact isotopic pattern distributions to corroborate experimental data. Conclusion We conclude that although ultra-high accurate mass instruments provide major insight into the chemical diversity of biological extracts, the facile annotation of a large proportion of signals is not possible by simple, automated query of current databases using computed molecular formulae. Parameterising MZedDB to take into account predicted ionisation behaviour and the biological source of any sample improves greatly both the frequency and accuracy of potential annotation 'hits' in ESI-MS data. en_US
dc.relation.ispartof BMC Bioinformatics en_US
dc.title Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules' en_US
dc.contributor.pbl Institute of Biological, Environmental and Rural Sciences en_US


Files in this item

Aside from theses and in the absence of a specific licence document on an item page, all works in Cadair are accessible under the CC BY-NC-ND Licence. AU theses and dissertations held on Cadair are made available for the purposes of private study and non-commercial research and brief extracts may be reproduced under fair dealing for the purpose of criticism or review. If you have any queries in relation to the re-use of material on Cadair, contact is@aber.ac.uk.

This item appears in the following Collection(s)

Show simple item record

Search Cadair


Advanced Search

Browse

Statistics