The Proteomics and Metabolomics Shared Resource (PMSR) at Georgetown University provides proteomics and metabolomics services and expertise. The document describes the PMSR's integrated proteomics workflow including 2D gel-based analysis, DIGE, spot picking, and MALDI TOF/TOF mass spectrometry for protein identification. Liquid chromatography-based proteomics using iTRAQ/ICAT labeling for quantitative analysis and a nano LC-QSTAR ELITE mass spectrometer are also described. The PMSR supports small molecule profiling and quantitation using UPLC-TOFMS and metabolomics applications.

1. Proteomics and Metabolomics Shared Resource (PMSR) Stephen Byers, PhD, Co-Director Al Fornace, MD, Co-Director Amrita Cheema, PhD, Metabolomics [email_address] Rado Goldman, Proteomics [email_address]

2. Proteomics: An Integrated Approach Gel Based Workflow LC Based Workflow Integrated Proteomics

3. 2D Gel Workflow Applications: Multiplexing of gels and visualization of differentially expressed spots between the sample and the control on the same gel. Differential Protein analysis: using the De Cyder Software. Improved spot detection: due to high sensitivity of the fluorescent labeling. Imager: used for other fluorescent imaging applications. DIGE Imager 2D DIGE ECL Plex Western Blot

4. Spot Picker Robotic spot picker: picks spots from 2D gels with increased accuracy efficiency based on the protein pick list generated by the image analysis software.

5. MALDI TOF-TOF Mass Spectrometers Applications: Identification of Proteins from complex biological samples using MASCOT. Supports LC MALDI workflows for isobaric labeling of proteins followed by identification. Serum Biomarker studies. In-Silico digest workflows for the analysis of post translational modifications. Nano LC coupled with Probotic Spotter 4800 Proteomics Analyzer

6. Nano Acquity UPLC- QSTAR ELITE LCMS/MS system Optimized for high throughput ‘ Shot gun’ proteomics workflows in conjunction with the online nano flow TEMPO MDLC system. High Speed data acquisition, database searching and processing Software. Ideally suited for quantitative proteomics using iTRAQ/ ICAT labeling methods for differential proteomic profiling

7. MALDI TOF-TOF Mass Spectrometers Ideally suited for quantitative proteomics using iTRAQ/ ICAT labeling methods for differential proteomic profiling. Detection of Post translational modifications. Serum Profiling studies made easy with marker view softwares for Principle component analysis. Metabolomics and metabolite detection. Detection and Identification of low abundance proteins due to high sensitivity and mass accuracy.

8. What Responses are Possible?

9. UPLC-TOFMS Applications: Small molecule profiling Small molecule quantization

10. Shared Resources are partially supported by the Georgetown Howard University Center for Clinical and Translational Studies (GHUCCTS) 1UL1RR031975-01 In your publications, remember to mention support provided from the GHUCCTS.