Mass Spectrometry (MS) Platforms and Software for Metabolomics
Untargeted “discovery” analysis
A discovery approach that aims to measure the broadest range of metabolites present in an extracted sample without a priori knowledge of the metabolome. Untargeted analysis can reveal novel metabolites associated with a phenotype and inform pathway analysis. In the Johnson lab we use high resolution liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) for untargeted analysis.
Targeted quantitative analysis
A quantitative hypothesis-driven approach to analyze a pre-defined set of metabolites of interest. Analysis is optimized to increase sensitivity and resolution of each metabolite. It can be used to validate untargeted metabolomic data and further expand metabolic pathway analysis. We use liquid chromatography triple quadrupole mass spectrometry (LC-QqQ-MS) for targeted analysis.
Mass spectrometry imaging
An in situ tissue analysis technique that reveals the spatial specificity of metabolites. Types of imaging we use include matrix-assisted laser desorption ionization (MALDI), nanostructure-imaging mass spectrometry (NIMS), and desorption electrospray ionization mass spectrometry (DESI). Imaging can also provide another level of validation.
XCMS Online data processing and pathway analysis
A one-shot automated metabolomic workflow that enables data upload, metabolite identification via METLIN, statistical analyses and pathway analysis. It features integrative systems biology analysis and acts as a repository with data sharing capabilities. https://xcmsonline.scripps.edu