Meharry Proteomics Core

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The Meharry Proteomics Core was established in order to provide services, computer resources, support, and training both inside and outside of the Meharry research community. Our goal is to ensure that all interested scientists are able to effectively exploit state-of-the-art mass spectrometric and computational technologies, especially related to the “omics” scale data-sets.

 

The Meharry Proteomics Core routinely performs LC-MS/MS applications such as complex protein/peptide analysis and shotgun proteomic profiling. We also analyze small molecule samples (lipids, metabolites, etc.). Additionally, we have ongoing partnerships with the MSRC Proteomics Lab at Vanderbilt University to offer more applications such as 2D Differential in Gel Electrophoresis (DIGE), relative protein quantification with mass tag or stable isotope labeling (iTRAQ/TMT or SILAC), Targeted Mass Spectrometry, Phosphoproteome analysis and Multidimensional LC-MS/MS (MudPIT).

Mission

Our Proteomics Core aids investigators and trainees with high performance computation in proteomics, as well as other “Omics” type applications needing efficient analysis of large-scale biological data sets.

 

Also, the Meharry Proteomics Core provides state of the art services, training and bioinformatics-driven data analysis to the Meharry translational research community.

 

It is our aim to keep this facility up to date computationally and intellectually with services to support education and research in proteomics, bioinformatics, computational biology, and systems biology.

 

The ability to incorporate proteomics into translational and clinical biomedical research is critical for the discovery of therapeutic interventions and high fidelity biomarkers of disease and response to therapy.

 

The objective of this component of our MeTRC Program is to establish a Proteomics Core facility, which will serve a broad research community and will significantly enhance translational and clinical research at Meharry Medical College. The establishment of this facility is significant in developing novel diagnostics and therapeutic interventions for infectious diseases critical to woman’s health.

To develop a Proteomics Core Facility to support Meharry’s clinical and translational research activities, and; to develop collaborations and partnerships inside and outside of Meharry Medical College that accelerate clinical and translational research, with the common link being the reliance on state-of-the-art proteomics strategies.

Based on the interest of current faculty in this resource, and their successes to date with proteomics in exploratory studies with collaborators at other institutions, we are confident that this investment will yield significant returns of discovery and fulfill basic-translational-clinical collaborations locally and nationally.

The Meharry Medical College Proteomics Core is funded by resources provided by the Research Centers in Minority Institutions (RCMI) and by the Meharry Medical College Clinical and Translational Research Center (MeTRC) programs of the National Institute on Minority Health and Health Disparities (NIMHD), a component of the National Institutes of Health (NIH).

Investigators, please cite this core appropriately in all abstracts, posters, papers and grant submissions:

“Experiments/Data analysis were performed by the Meharry Medical College Proteomics Core, which is supported in part by the Research Centers in Minority Institutions Program (RCMI) grant G12 MD007586 and by the Meharry Clinical and Translational Research Center (MeTRC) grant U54 MD007593 from the National Institute on Minority Health and Health Disparities (NIMHD) of the NIH.”

Hardware

  • ThermoFinnegan LTQ LinearIon Trap Mass Spectrometer
  • AB Sciex Tempo Nano-1D plus nano-HPLC
  • AB Sciex 920 Autosampler with cooling module
  • Custom NanoSPRAY ESI source (James A. Hill Company)

Software

  • Thermo Scientific Xcalibur Mass Spectrometry Controller Software
  • Thermo Scientific Proteome Discoverer Mass Informatics Platform Software
  • MATLAB programming environment with bioinformatics, statistics and proteomics analysis suites
  • CYTOSCAPE bioinformatics software for systems biology and biological pathway interaction network analysis

Services

Liquid Chromotography Multistage Mass Spectrometry. Basic Analysis includes sample preparation and identification of trypsinized protein samples.

profiling and identification of complex protein samples.

LC/MS/MS analyses from gel bands or spots.

LC/MS and LC/MS/MS analyses (qualitative and quantitative) of small bio-molecules (peptides, drugs, metabolites, vitamins, etc.)

2D Differential In-Gel Electrophoresis (DIGE), Targeted Mass Spectrometry and Multidimensional LC/MS/MS (MudPIT) – available via the partnerships with the MSRC Proteomics Lab at the Vanderbilt University.

Meharry Proteomics Core personnel provide consulting to enable investigators to frame research questions in proteomics terms and identify solutions to those questions. Core personnel are then available to facilitate these solutions.

Sample Protocol (Protein in-gel Digestion Protocol)

Meharry Proteomics Core personnel enable grant submission by helping to identify proteomic and bioinformatic approaches to investigators’ research problems, framing the questions in “Omics” terms and providing letters of support that indicate sufficient expertise and tools exist to successfully complete the research indicated.

Whenever possible, data analysis is approached as a training opportunity. However, there are times when this is undesirable either due to the complexity of the data (and analysis options) or the wishes of the investigator. In these instances, we do perform data analysis but request the participation of the investigator, as an appropriate analysis requires a fundamental understanding of the biology and experiment, which can only be supplied by the person who has done the work.

As proteomics/bioinformatics needs arise in the research community or in individual laboratories, core personnel will help identify and make available resources that will address these needs. We will also train persons to use these resources effectively.

Core personnel provide training primarily in one-on-one or small group settings. We also provide workshops for specific bioinformatics packages or approaches to larger groups as needs are identified that can be addressed in this format. Talks have been and continue to be presented to departments to inform investigators of the value of proteomics & bioinformatics to their research and the services that are provided by the Proteomics Core.

To request services, please fill out the submission form and send it to:

Siddharth Pratap Ph.D.
Bioinformatics and Proteomics Core Director
spratap@mmc.edu
615.327.6219

Proteomics Core Staff

Siddharth Pratap

Siddharth Pratap, Ph.D.

Assistant Professor and Director, Bioinfomatics
Graduate Studies and Research

Phone: 615.327.6219
Email: spratap@mmc.edu

View Publications

Victor Paromov

Victor Paromov Ph.D.

Proteomics Core Associate Manager
Associate Managing Director, MeTRC
Microbiology and Immunology
School: Medicine

Phone: 615.327.6564
Email: vparomov@mmc.edu