Facility Details

The VAI Mass Spectrometry Core (MSC) is committed to developing scientific partnerships with research labs to develop and deploy LC/MS and GC/MS methods specifically tailored to meet the needs of every project. The MSC houses a comprehensive suite of technologies and staff expertise to deliver high quality metabolomics, lipidomics, and proteomics capabilities to VARI scientists and collaborators. The process begins with experimental design support to ensure samples are handled properly, necessary controls are included, and the study is sufficiently powered. Analytical capabilities are combined with custom informatics and statistics solutions to enable faster analysis and more approachable data interpretation. Specific capabilities in the MSC include:

Metabolomics and Lipidomics – Three liquid chromatography-mass spectrometry (LC/MS) systems (Thermo Orbitrap ID-X, Thermo Orbitrap Exploris 240, and Agilent 6470 QQQ) and three gas chromatography (GC)/MS systems (Agilent 5977b (2), Thermo 7610 ISQ) are dedicated to small molecule analysis. These instruments deploy an array of standard methods, annotated with a chemical library of over 1000 compounds, to maximize compound coverage in every sample. For metabolomics these methods routinely detect 200+ compounds including TCA cycle intermediates, glycolysis, nucleotides, amino acids, urea cycle, vitamins, cofactors tryptophan/kynurenine metabolism, acyl-CoA’s, acyl-carnitines, polyamines, and others. For lipidomics, 500+ lipid species are routinely annotated including phospholipids, ceramides, triacylglycerides, cardiolipins, cholesterol esters, and more. These methods can be operated in an untargeted manner, allowing for screening for biomarkers and novel metabolites/lipids, and in the context of stable isotope tracing, which allows for assessment of metabolic movement. Further, in line with the scientific partnership mission of the MSC, custom methods are routinely developed to quantitate project-specific compounds of interest.

Proteomics – Two nano LC/MS systems (Orbitrap Eclipse and Orbitrap Exploris 480) are dedicated to protein analysis. The expertise and instrumentation will readily make available many proteomics applications including bottom-up quantitative proteomics, tandem mass-tag proteomics, post-translational modification analysis (including phosphoproteomics and histone PTM characterization), protein-protein interactions, intact protein structural elucidation, and more..

Bioinformatics – The MSC has a staff bioinformatician who is dedicated to developing and maintaining informatics pipelines for mass spectrometry data analysis and visualization. This custom data visualization platform transforms daunting excel documents into communicative and interactive figures. Additional layers of data and analysis available through an intuitive user interface, researchers can dive as deep into metabolic pathways and quantitative analyses as demanded by their research questions. Flexible and comprehensive data reporting allows clients to download processed data in excel as well as figures for publication and presentation. The bioinformatician further enables project specific informatics and statistics solutions to ensure robust and informative results for every research question.

Major equipment in the facility includes:
• Thermo Scientific Orbitrap ID-X LC/MS
• Thermo Scientific Orbitrap Exploris 240 LC/MS
• Thermo Scientific Orbitrap Eclipse nanoLC/MS
• Thermo Scientific Orbitrap Exploris 480 nanoLC/MS
• Agilent 6470 Triple Quadrupole LC/MS
• Agilent Infinity 1290II UPLC
• Agilent 5977B GC/MS (2)
• Thermo Scientific ISQ7610 EI/CI enabled GC/MS