Computational protocol: Metabolic Biomarkers of Ageing in C57BL/6J Wild-Type and Flavin-Containing Monooxygenase 5 (FMO5)-Knockout Mice

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Protocol publication

[…] Metabolite identification was carried out using standard methods (Dona et al., ) and using information from the literature and public databases including the Chenomx NMR Suite (http://www.chenomx.com/), the Human Metabolite Database (HMDB, http://www.hmdb.ca/) (Wishart et al., ), the Biological Magnetic Resonance Data Bank (BMRB, http://www.bmrb.wisc.edu/metabolomics/) (Ulrich et al., ), the Birmingham Metabolite Library (BML, http://www.bml-nmr.org/) (Ludwig et al., ), and COLMAR (Complex Mixture Analysis by NMR, http://spin.ccic.ohio-state.edu/index.php/colmarm/index) (Bingol et al., ). A series of 2D NMR experiments, including J-resolved, correlation spectroscopy (COSY), TOCSY, HSQC, and HMBC (Claridge, ), were acquired for a number of samples in order to assist or confirm the identification of a range of metabolites. The identities of the key discriminating metabolites were also confirmed by the spiking of authentic standards into urine and plasma samples. Confidence in the identification of these known metabolites was assessed using the new metabolite identification carbon efficiency (MICE) (Everett, ) and topological MICE (tMICE) (Sanchon-Lopez and Everett, ) methods. […]

Pipeline specifications

Software tools Chenomx NMR Suite, COLMAR
Databases HMDB
Application NMR-based metabolomics
Organisms Mus musculus, Homo sapiens
Chemicals Taurine