The metabolomics laboratories include standard equipment for chemical synthesis (chemical hoods) and metabolite analysis. Major equipment include: two standard quadrupole Agilent 5977B gas chromatograph-mass spectrometry (GCMS)-based systems that each have a high sensitivity, high efficiency source with both electron impact and chemical ionization capability, and well as two Agilent 5975C gas chromatograph-mass spectrometers (GC-MS) that are used for the bulk of the broad spectrum metabolomic analyses; and a ThermoFinnigan Polaris GCQ (ion trap) GC-MS, a high resolution (accurate mass) ThermoFisher Q Exactive Orbitrap GC-MS/MS, and a Waters accurate mass GCT Premier Time-of-Flight GC-MS. These instruments provide the capability to do broad spectrum metabolite profiling and elucidation of unknown metabolites. For metabolite structural elucidation, an Avance 400 MHz wide-bore multinuclear NMR is accessible. Additionally, LC-MS instrumentation is also accessible and includes a Waters Synapt High Definition (HD) MS system and a Sciex API 4000 QTrap Plus. The Synapt HDMS is a hybrid Quadrupole-Time-of-Flight MS that can be used for metabolite discovery. All ‘omic informatics efforts, including data processing, database searching, analyte quantification, data dissemination (via web-based portals) and data storage, are handled in an automated, in-house constructed/maintained proteome/metabolite informatics pipeline.
Pictured above (left) are high performance liquid chromatography- ThermoFisher Astral and QExactive-Plus mass spectrometry instrumentation, equipped for nanoflow electrospray ionization. These platforms provide high resolution, high mass accuracy measurements of proteomes and metabolomes from complex plant-microbiome samples, thereby providing detailed information on the functional dynamics in this inter-kingdom interaction.