John M. Koomen, Ph.D.
Assistant Professor, Department of Interdisciplinary Oncology
Scientific Director, Proteomics Core Facility
Member-in-Residence of the Moffitt Cancer Center
E-mail: John.Koomen@moffitt.org
Phone: (813)745-8524
Training
Ph.D. Texas A & M University 2002
Research
Interests
Research in the Koomen lab focuses on developing methods for proteomic analysis and evaluating their effectiveness and the validity of the results with functional investigations. After defining the biological problem of interest, existing analytical strategies are reviewed. Modified versions of existing approaches or novel techniques are then investigated and subsequently applied. Currently, we are examining chemical cleavage mechanisms for proteomics research and isolated organ perfusion coupled with proteomics for candidate biomarker discovery.
One of the most promising techniques for proteome analysis is liquid chromatography-mass spectrometry (LC-MS) profiling. In this semi-quantitative technique, the peptides created by enzymatic digestion (typically with trypsin) are separated by their reverse phase retention time and the mass-to-charge ratio (an experimental measurement of their molecular weight). Statistical analysis of the intensities of each peak can be used to determine which peptide ion signals differ between experimental groups. These targets are then sequenced with tandem mass spectrometry to identify their protein of origin. The lists of proteins then are analyzed by comparison to the existing literature to select candidates for further functional investigations. One of the major bottlenecks in this process is peak capacity. In other words, you can only observe so many peptides in any given LC-MS analysis. This number has been shown to be between 8,000 and 20,000 in reverse phase separations of tryptic peptides. Chemical cleavages and additional proteolytic enzymes are being investigated to complement trypsin in the sample preparation steps of mass spectrometry profiling.
For candidate biomarker discovery, s elected mouse organs, including liver and kidney, will be inoculated with human tumor cells. After tumors develop, the organs will be isolated ex vivo and perfused with protein-free buffer. Broadband protein identification and quantitation methods will be used to determine which tumor-related (human) and host response (mouse) proteins are observed in the effluent of these tumor-bearing organs. From the list of protein identities, candidate biomarkers will be selected based on organ specificity, tumor specificity, and protein function; these markers will be further investigated using immunohistochemistry and validated by antibody-based methods in human sera from large populations of cancer patients and corresponding controls.
Additional projects include development and application of novel methods to isolate selected compartments of the proteome and optimization of sample preparation strategies for mass spectrometry analysis.
Search
for publications by: 
This
search will be conducted at the US National Library of Medicine (NLM) and PubMed.
Selected Publications
Morris JS, Coombes KR, Koomen J, Baggerly KA, Kobayashi R. Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum. Bioinformatics. 2005, 21(9), 1764-75. Epub 2005 Jan 26.
He G, Siddik ZH, Huang Z, Wang R, Koomen J, Kobayashi R, Khokhar AR, Kuang J. Induction of p21 by p53 following DNA damage inhibits both Cdk4 and Cdk2 activities. Oncogene. 2005, 24(18), 2929-43.
Koomen JM, Zhao H, Li D, Nasser W, Hawke DH, Abbruzzese JL, Baggerly KA, Kobayashi R. Diagnostic protein discovery using liquid chromatography/mass spectrometry for proteolytic peptide targeting. Rapid Commun Mass Spectrom. 2005, 19(12), 1624-36.
Koomen JM, Li D, Xiao LC, Liu TC, Coombes KR, Abbruzzese J, Kobayashi R. Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. J Proteome Res. 2005 May-Jun, 4(3), 972-81.
Koomen JM, Wilson CR, Guthrie P, Androlewicz MJ, Kobayashi R, Taegtmeyer H. Proteome Analysis of Isolated Perfused Organ Effluent as a Novel Model for Protein Biomarker Discovery. J Proteome Res. 2006 Jan 6;5(1):177-182.
Cancer Biology Ph.D. Program
H. Lee Moffitt Cancer Center, MRC-4 East
12902 Magnolia Drive
Tampa, Florida 33612
Phone: 813-745-6876
E-mail: CancerPHD@moffitt.org
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