The Metabolomics Lab is equipped with high-throughput robotic systems for the analysis of
large samples sets. Data analysis is performed using a number of commercial
and home build software tools for the discovery of biomarkers and metabolic
signatures of disease, toxicity or other biological outcomes.
The raw NMR data is processed using a number of commercial NMR software packages, including ACD NMR Processor (ACD Lab, Toronto, Canada), Varian VNMRJ-CRAFT (Varian Inc., Palo Alto, CA), Chenomx (Edmonton, Canada) and Spinworks (Univ. of Manitoba, Canada)
The processed NMR data is then exported for multivariate statistical analysis, including principal component analysis (PCA), projection to latent structures (PLS), orthogonal-PLS (OPLS) and support vector machine analysis (SVM). Additional methods are currently under development. The statistical software utilized by the lab includes SimcaP+ (Umetrics, Umea, Sweden), R. and Matalab (Mathworks, Natick, MA).
What can we see?
NMR is an “unbiased” detector in that essentially any organic compound (containing a hydrogen atom) of sufficient quantity can be detected. Typically we readily see compounds with concentrations ranging from low micromolar up through millimolar levels. For highly dilute samples that can be lyophilized, we can re-suspend the samples in a smaller volume (10µl) and analyze the sample using the micro-coil system. This can effectively bring the detection limit down several orders of magnitude.
We use the Chenomx NMR database in our analysis that allows us to get absolute quantitation on nearly 300 metabolites including, amino acids, organic acids, amines, nucleic acids, carbohydrates, drug related metabolites, etc. We also use online NMR databases to confirm identities such as the human metabolome and Wisconsin metabolome web sites.
For unknown compounds we run multidimensional NMR experiments (e.g. gDQCOSY, gTOCSY, gHSQC, gHMBC, selective TOCSY, etc) which yield spectra containing a wealth structural information for the elucidation of novel & unknown metabolites