COBRE in Mesenchymal and Neural Regulation of Metabolic Networks

COBRE Core Facility

The Proteomics and Lipidomics Core —  Dr. Cal Vary

The Proteomics and Lipidomics Core focuses on molecular characterization of protein and lipid changes in cells and complex tissues. As a component of this COBRE, we provide support to define protein and lipid signatures in adipose tissue, blood, marrow serum, bone, and nervous tissue.  We house a triple quadrupole linear ion trap mass spectrometer to enhance protein quantitative and metabolite analysis (4000QTRAP, Sciex). In addition to a dual probe (DuoSpray) electrospray source for lipid analyses, this instrument can be alternatively fitted with a Nanospray III source for high sensitivity protein identification and quantitative analysis in MRM mode. We also house a Sciex 5600 triple-TOF instrument. The triple-TOF 5600 and the 4000QTRAP share a U_3000 RSLC nanoscale liquid chromatographic system, with a multi-tray autosampler that has greatly facilitated automated medium throughput for TOF- and TRAP-based analyses. The triple-TOF 5600 mass spectrometer acquisition has positioned us to maximally exploit versatile new state-of-the-art scanning data acquisition modalities such as SWATH (protein) and MS/MSALL (lipids), whereas the QTRAP provides the ideal platform for targeted analysis of specific lipid or protein molecules. These allow us to address emerging protein analytics by combining the high speed scanning capabilities of the triple TOF instrument for initial unbiased SWATH proteomics and MS/MSALL lipidomics discovery with subsequent targeted quantitative protein and lipid analysis using MRM (4000QTRAP). Thus, this combination of instruments is particularly well suited to support the projects in this COBRE, as well as provide expertise to support projects outside of our institution. For more information, contact Dr. Calvin Vary (

Capabilities of this core facility and support for the COBRE projects is indicated below: