The Metabolomics Core at Baylor College of Medicine is an analytical facility specializing in liquid chromatography hyphenated with mass spectrometry techniques. Its main role is to support investigators in their research in the study of metabolism, as well as understanding of the mechanisms of particular cancer states, which will ideally lead to earlier detection and better treatments. The core has established methods for targeted measurement of over 500 metabolites, metabolic flux, and drug metabolism and pharmacokinetics (DMPK) in diverse biological specimens using established protocols, methods and mass spectrometry as the primary platform.
Procedurally, the core personnel perform extraction of metabolites from biological samples using a combination of aqueous and organic solvents, carry out the mass spectrometry analysis, and pre-process the mass spectral data. The entire process starting from sample preparation to mass spectrometry is monitored using spiked isotopic standards that have been characterized for their chromatographic behavior and fragmentation profile. Once the mass spectral data is obtained, various data analytics steps namely scaling, imputation and normalization are performed using Mass Hunter software and the resulting output is passed on to an in-house biostatistics pipeline, that then computes the data to determine metabolite levels, and define differential compounds. This Tier 1 level of data analysis is provided as part of routine Core service. Upon request, additional advanced Tier 2 level data analysis can be provided separately by our bioinformatics group. Tier 2 analysis can include pathway mapping using multiple enrichment methods that include Oncomine Concept Map (OCM), Ingenuity (IPA), Gene Set Analysis (GSA), and Network-based Gene Set Enrichment Analysis (NETGSEA). Tier 2 data analysis can also support integration of transcriptomic and proteomic data (if available with the investigator) with the metabolomics data.