Metabolomics Solution

Several crucial steps are important for confidently identifying compounds relevant for dynamic metabolic processes; including sample preparation, data acquisition and data evaluation. Meaningful insights in a biological context can only be obtained if all of these workflow steps are controlled. To simplify and harmonize these, Bruker, in collaboration with Prof. Liang Li and his team at the University of Alberta, Canada, have developed the T-ReX^® LC-QTOF solution.

The first critical step in non-targeted metabolomics is a reproducible sample preparation. Hence, Standard Operation Procedures (SOPs) for preparing typical clinical research samples, including urine and plasma, are provided as part of this metabolomics solution.

Acquisition of high quality LC-MS/MS data follows sample preparation in non-targeted metabolomics workflows, with the T-ReX^® LC-QTOF solution, no LC-MS/MS parameter optimization is required. To analyze large sample cohorts which require high retention time stability the Elute UHPLC  in combination with the dedicated T-ReX^® Elute Metabolomics-kit: RP is provided. The Reversed-Phase LC column kit enables matching of retention times to values in the Bruker HMDB Metabolite Library 2.0. The impact II for MS/MS data acquisition uses optimized parameters and its robust performance is the basis for high quality data acquisition, enabling extensive profiling studies of complex samples.

Following data acquisition, the MetaboScape^® software provides streamlined data evaluation, enabling automatic and confident identification of relevant known compounds:

• Unique T-ReX^® 3D feature extraction technology is the key to subsequent metabolite identification and statistical data evaluation. By automatically conducting parameter free retention time alignment and region complete extraction, all relevant information is extracted to enable confident metabolite identification and at the same time false negative rate in statistical analysis is reduced.

• The Bruker HMDB Metabolite Library 2.0 as part of this metabolomics solution provides MS/MS spectra for >800 metabolites with retention time information for >600 relevant metabolites. The library is a prerequisite for confident identification of relevant markers.

• In-silico generated MS/MS spectra in the Bruker MetaboBASE^® Personal Library 3.0 enables tentative identification of relevant targets which are not yet available as pure reference standards.

• Annotation Quality (AQ) scoring provides a fast overview giving confidence in each annotation parameter.

• Pathway mapping functionality enables the setting of identified compounds into a biological context.

Phenotyping by Magnetic Resonance Mass Spectrometry (MRMS)

A deep metabolic profiling of complex mixtures for discovery metabolomics in the context of phenotyping is enabled by UHPLC-QTOF-MS/MS analyses. Typically different LC methods and data acquisition in positive and negative ion mode are combined which comes at a cost; the time required for each sample analyzed.  
Magnetic Resonance Mass Spectrometry (MRMS) eXtreme Resolution enables acceleration of sample throughput in phenomics and discovery metabolomics research by omitting time consuming chromatography. Flow Injection Analysis (FIA) or MALDI based workflows provide access to compounds not readily detectable by LC-MS analysis and simultaneously analyze known and unknown metabolites.
For high-throughput needs, as typically encountered in phenomics research, UHPLC-QTOF-MS/MS analyses are complemented by MRMS aXelerate, an LC-free MRMS workflow solution which detects and generates molecular formulae for >1,000 medium-high level metabolites per sample and reveals many extra metabolites not seen in LC-MS, including polar compounds. MRMS analysis by FIA or MALDI provides high sample throughput for phenotyping of complex samples (e.g. urine and plasma extracts). The powerful data extraction by T-ReX^® 2D in MetaboScape^® provides confidence in automatic annotation. This is achieved by mass accuracy of <0.2 ppm and mass resolution which can exceed >1 million and thus boosts isotopic fine structure fidelity.

Learn in this recent publication how the FIA-CASI-MRMS workflow helped to address the quest to illuminate the “dark metabolic matter” by a 2.6-fold increase in both matching with the Human Metabolome Database and an increase in the IFS pattern: An Enhanced Isotopic Fine Structure Method for Exact Mass Analysis in Discovery Metabolomics: FIA-CASI-FTMS