Proteomics and Metabolomics Laboratory

Capabilities overview

Metabolomics

The Metabolomics Core is equipped with a State-of-the -Art tandem mass spectrometry systems that are dedicated to the analysis of small molecule metabolites. The core can carry out both targeted and untargeted metabolomic experiments. The core operates on both a fee-for-service basis and an independent use basis. For fee-for-service experiments, we ask that investigators initially consult with core personnel prior to sample submission. Every experimental step from sample preparation to data analysis is performed by Core personnel. Alternatively, investigators can be trained to operate the instrument and perform data analysis. Several contract options are available for users interested in learning to perform their own experiments. Expert technical assistance tailored to meet the needs of investigators in all aspects of the studies can be provided for investigators who are either novices or knowledgeable in mass spectrometry applications. This includes advice in methods of appropriate sample storage and preparation, and assistance in HPLC or LC/MS/MS based method development.

Proteomics

The Proteomics Core is a protein sequencing facility that uses tandem mass spectrometry methods to sequence and identify proteins. The Core is equipped with two capillary column HPLC electrospray ionization-ion trap mass spectrometry systems, a high resolution ThermoFinnigan Orbitrap Elite and a ThermoFinnigan LTQ instruments. These instruments are dedicated to high sensitivity protein and peptide analyses. The Core routinely analyzes gel separated proteins that have been stained with either Coomassie-blue or silver. In addition, investigators can submit isolated proteins for in-solution digestion and analysis. The Core provides several proteomic services including protein identification, protein quantitation, post-translational modification analysis including quantitation, and proteome dynamic studies. The workflow of the lab includes sample digestion, liquid chromatography tandem mass spectrometry, data analysis, and a written report is provided for all samples. The turnaround time for most samples is two weeks. The laboratory has off-line data analysis stations and several database search programs including Proteome Discoverer, Mascot, Sieve, and Scaffold that facilitate both the identification and quantitation experiments. The Proteomics Core is partly supported by the Case Comprehensive Cancer Center.