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John Koomen

Assistant Professor/Scientific Director of Proteomics Core - Proteomics Core Facility
Tampa Florida, US

BS in Biology from Guilford College in 1995
MS in Biochemistry and Molecular Biology from the University of Texas at Houston Graduate School of Biomedical Sciences in 1998, mentored by Richard Caprioli, PhD
PhD in Chemistry from Texas A&M University in 2002, mentored by David H. Russell, PhD
Work Experience
2002-2005 Research Associate, then Instructor MD Anderson Cancer Center, mentored by Ryuji Kobayashi, PhD
2005-present Assistant Professor, Moffitt Cancer Center

Position - Company  
Assistant Professor/Scientific Director of Proteomics Core - Proteomics Core Facility H. Lee Moffitt Cancer Center and Research Institute Jul 2005 - Present
Degree - University  
PhD, Chemistry - Texas A&M University 1998 - 2002
Publication Info
Charting the Landscape of Tandem BRCT Domain-Mediated Protein Interactions. Woods NT, Mesquita RD, Sweet M, Carvalho MA, Li X, Liu Y, Nguyen H and 6 others Sci Signal. 5(242):rs6. doi: 10.1126/scisignal.2002255. September 18, 2012. View on PubMed.
Stemness of B cell progenitors in multiple myeloma bone marrow. Boucher K, Parquet N, Widen R, Shain KH, Baz R, Alsina M, Koomen J, Anasetti C, Dalton WS, Perez L Clin Cancer Res. :. doi: 10.1158/1078-0432.CCR-12-0531. September 17, 2012. View on PubMed.
H2B Tyr37 phosphorylation suppresses expression of replication-dependent core histone genes. Mahajan K, Fang B, Koomen JM, Mahajan NP Nat Struct Mol Biol. 19(9):930-7. doi: 10.1038/nsmb.2356. September 2012. View on PubMed.
GSK3β Inhibition Blocks Melanoma Cell/Host Interactions by Downregulating N-Cadherin Expression and Decreasing FAK Phosphorylation. John JK, Paraiso KH, Rebecca VW, Cantini LP, Abel EV, Pagano N, Meggers E and 8 others J Invest Dermatol. :. doi: 10.1038/jid.2012.237. July 19, 2012. View on PubMed.
SIRT1 negatively regulates the activities, functions, and protein levels of hMOF and TIP60. Peng L, Ling H, Yuan Z, Fang B, Bloom G, Fukasawa K, Koomen J, Chen J, Lane WS, Seto E Mol Cell Biol. 32(14):2823-36. doi: 10.1128/MCB.00496-12. July 2012. View on PubMed.
An ET-CURE Pilot Project Supporting Undergraduate Training in Cancer Research, Emerging Technology, and Health Disparities. Wilson DS, Fang B, Dalton WS, Meade CD, Koomen JM J Cancer Educ. 27(3):418-27. doi: 10.1007/s13187-012-0362-z. June 2012. View on PubMed.
Phosphoproteomics identifies driver tyrosine kinases in sarcoma cell lines and tumors. Bai Y, Li J, Fang B, Edwards A, Zhang G, Bui M, Eschrich S, Altiok S, Koomen J, Haura EB Cancer Res. 72(10):2501-11. doi: 10.1158/0008-5472.CAN-11-3015. May 15, 2012. View on PubMed.
The HSP90 inhibitor XL888 overcomes BRAF inhibitor resistance mediated through diverse mechanisms. Paraiso KH, Haarberg HE, Wood E, Rebecca VW, Chen YA, Xiang Y, Ribas A and 7 others Clin Cancer Res. 18(9):2502-14. doi: 10.1158/1078-0432.CCR-11-2612. May 1, 2012. View on PubMed.
Evaluation of direct infusion-multiple reaction monitoring mass spectrometry for quantification of heat shock proteins. Xiang Y, Koomen JM Anal Chem. 84(4):1981-6. doi: 10.1021/ac203011j. February 21, 2012. View on PubMed.
Evaluation of protein quantification using standard peptides containing single conservative amino acid replacements. Remily-Wood ER, Koomen JM J Mass Spectrom. 47(2):188-94. doi: 10.1002/jms.2053. February 2012. View on PubMed.
A mass spectrometry-based method to screen for α-amidated peptides. An Z, Chen Y, Koomen JM, Merkler DJ Proteomics. 12(2):173-82. doi: 10.1002/pmic.201100327. January 2012. View on PubMed.
Molecular mechanism of glyceraldehyde-3-phosphate dehydrogenase inactivation by α,β-unsaturated carbonyl derivatives. Martyniuk CJ, Fang B, Koomen JM, Gavin T, Zhang L, Barber DS, Lopachin RM Chem Res Toxicol. 24(12):2302-11. doi: 10.1021/tx200437y. December 19, 2011. View on PubMed.
SIRT1 deacetylates the DNA methyltransferase 1 (DNMT1) protein and alters its activities. Peng L, Yuan Z, Ling H, Fukasawa K, Robertson K, Olashaw N, Koomen J, Chen J, Lane WS, Seto E Mol Cell Biol. 31(23):4720-34. doi: 10.1128/MCB.06147-11. December 2011. View on PubMed.
MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a. Chang Y, Sun L, Kokura K, Horton JR, Fukuda M, Espejo A, Izumi V and 6 others Nat Commun. 2:533. doi: 10.1038/ncomms1549. November 15, 2011. View on PubMed.
Monitoring a nuclear factor-κB signature of drug resistance in multiple myeloma. Xiang Y, Remily-Wood ER, Oliveira V, Yarde D, He L, Cheng JQ, Mathews L and 9 others Mol Cell Proteomics. 10(11):M110.005520. doi: 10.1074/mcp.M110.005520. November 2011. View on PubMed.
A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. Remily-Wood ER, Liu RZ, Xiang Y, Chen Y, Thomas CE, Rajyaguru N, Kaufman LM and 15 others Proteomics Clin Appl. 5(7-8):383-96. doi: 10.1002/prca.201000115. August 2011. View on PubMed.
Using quantitative proteomic analysis to understand genotype specific intrinsic drug resistance in melanoma. Koomen JM, Smalley KS Oncotarget. 2(4):329-35. doi: 10.18632/oncotarget.263. April 2011. View on PubMed.
PTEN loss confers BRAF inhibitor resistance to melanoma cells through the suppression of BIM expression. Paraiso KH, Xiang Y, Rebecca VW, Abel EV, Chen YA, Munko AC, Wood E and 9 others Cancer Res. 71(7):2750-60. doi: 10.1158/0008-5472.CAN-10-2954. April 1, 2011. View on PubMed.
Cdc45 limits replicon usage from a low density of preRCs in mammalian cells. Wong PG, Winter SL, Zaika E, Cao TV, Oguz U, Koomen JM, Hamlin JL, Alexandrow MG PLoS One. 6(3):e17533. doi: 10.1371/journal.pone.0017533. March 1, 2011. View on PubMed.
Mass spectrometry mapping of epidermal growth factor receptor phosphorylation related to oncogenic mutations and tyrosine kinase inhibitor sensitivity. Zhang G, Fang B, Liu RZ, Lin H, Kinose F, Bai Y, Oguz U and 6 others J Proteome Res. 10(1):305-19. doi: 10.1021/pr1006203. January 7, 2011. View on PubMed.
Characterizing tyrosine phosphorylation signaling in lung cancer using SH2 profiling. Machida K, Eschrich S, Li J, Bai Y, Koomen J, Mayer BJ, Haura EB PLoS One. 5(10):e13470. doi: 10.1371/journal.pone.0013470. October 19, 2010. View on PubMed.
Critical role of Shp2 in tumor growth involving regulation of c-Myc. Ren Y, Chen Z, Chen L, Fang B, Win-Piazza H, Haura E, Koomen JM, Wu J Genes Cancer. 1(10):994-1007. doi: 10.1177/1947601910395582. October 2010. View on PubMed.
Methods for investigation of targeted kinase inhibitor therapy using chemical proteomics and phosphorylation profiling. Fang B, Haura EB, Smalley KS, Eschrich SA, Koomen JM Biochem Pharmacol. 80(5):739-47. doi: 10.1016/j.bcp.2010.03.027. September 1, 2010. View on PubMed.
Quantification of beta-catenin signaling components in colon cancer cell lines, tissue sections, and microdissected tumor cells using reaction monitoring mass spectrometry. Chen Y, Gruidl M, Remily-Wood E, Liu RZ, Eschrich S, Lloyd M, Nasir A and 5 others J Proteome Res. 9(8):4215-27. doi: 10.1021/pr1005197. August 6, 2010. View on PubMed.
MDM2 recruitment of lysine methyltransferases regulates p53 transcriptional output. Chen L, Li Z, Zwolinska AK, Smith MA, Cross B, Koomen J, Yuan ZM and 4 others EMBO J. 29(15):2538-52. doi: 10.1038/emboj.2010.140. August 4, 2010. View on PubMed.
Wavelet-based adaptive denoising and baseline correction for MALDI TOF MS. Shin H, Sampat MP, Koomen JM, Markey MK OMICS. 14(3):283-95. doi: 10.1089/omi.2009.0119. June 2010. View on PubMed.
A chemical and phosphoproteomic characterization of dasatinib action in lung cancer. Li J, Rix U, Fang B, Bai Y, Edwards A, Colinge J, Bennett KL and 6 others Nat Chem Biol. 6(4):291-9. doi: 10.1038/nchembio.332. April 2010. View on PubMed.
Urine collection and processing for protein biomarker discovery and quantification. Thomas CE, Sexton W, Benson K, Sutphen R, Koomen J Cancer Epidemiol Biomarkers Prev. 19(4):953-9. doi: 10.1158/1055-9965.EPI-10-0069. April 2010. View on PubMed.
Ack1 mediated AKT/PKB tyrosine 176 phosphorylation regulates its activation. Mahajan K, Coppola D, Challa S, Fang B, Chen YA, Zhu W, Lopez AS and 9 others PLoS One. 5(3):e9646. doi: 10.1371/journal.pone.0009646. March 19, 2010. View on PubMed.
IKKepsilon phosphorylation of estrogen receptor alpha Ser-167 and contribution to tamoxifen resistance in breast cancer. Guo JP, Shu SK, Esposito NN, Coppola D, Koomen JM, Cheng JQ J Biol Chem. 285(6):3676-84. doi: 10.1074/jbc.M109.078212. February 5, 2010. View on PubMed.
Activation of the unfolded protein response contributes toward the antitumor activity of vorinostat. Kahali S, Sarcar B, Fang B, Williams ES, Koomen JM, Tofilon PJ, Chinnaiyan P Neoplasia. 12(1):80-6. January 2010. View on PubMed.
Acid hydrolysis of proteins in matrix assisted laser desorption ionization matrices. Remily-Wood E, Dirscherl H, Koomen JM J Am Soc Mass Spectrom. 20(11):2106-15. doi: 10.1016/j.jasms.2009.07.007. November 2009. View on PubMed.
IPEP: an in silico tool to examine proteolytic peptides for mass spectrometry. Lu D, Liu RZ, Izumi V, Fenstermacher D, Haura EB, Koomen J, Eschrich SA Bioinformatics. 24(23):2801-2. doi: 10.1093/bioinformatics/btn511. December 1, 2008. View on PubMed.
Proteomic contributions to personalized cancer care. Koomen JM, Haura EB, Bepler G, Sutphen R, Remily-Wood ER, Benson K, Hussein M and 7 others Mol Cell Proteomics. 7(10):1780-94. doi: 10.1074/mcp.R800002-MCP200. October 2008. View on PubMed.
Parametric power spectral density analysis of noise from instrumentation in MALDI TOF mass spectrometry. Shin H, Mutlu M, Koomen JM, Markey MK Cancer Inform. 3:219-30. September 17, 2007. View on PubMed.
HDAC6 modulates cell motility by altering the acetylation level of cortactin. Zhang X, Yuan Z, Zhang Y, Yong S, Salas-Burgos A, Koomen J, Olashaw N and 6 others Mol Cell. 27(2):197-213. doi: 10.1016/j.molcel.2007.05.033. July 20, 2007. View on PubMed.
Pre-analytic saliva processing affect proteomic results and biomarker screening of head and neck squamous carcinoma. Ohshiro K, Rosenthal DI, Koomen JM, Streckfus CF, Chambers M, Kobayashi R, El-Naggar AK Int J Oncol. 30(3):743-9. March 2007. View on PubMed.
A method for the isolation of blocked N-terminal peptides. Coussot G, Hawke DH, Mularz A, Koomen JM, Kobayashi R Anal Biochem. 361(2):302-4. doi: 10.1016/j.ab.2006.11.024. February 15, 2007. View on PubMed.
Upregulation of p27 and its inhibition of CDK2/cyclin E activity following DNA damage by a novel platinum agent are dependent on the expression of p21. He G, Kuang J, Huang Z, Koomen J, Kobayashi R, Khokhar AR, Siddik ZH Br J Cancer. 95(11):1514-24. doi: 10.1038/sj.bjc.6603448. December 4, 2006. View on PubMed.
Involvement of the conserved adaptor protein Alix in actin cytoskeleton assembly. Pan S, Wang R, Zhou X, He G, Koomen J, Kobayashi R, Sun L, Corvera J, Gallick GE, Kuang J J Biol Chem. 281(45):34640-50. doi: 10.1074/jbc.M602263200. November 10, 2006. View on PubMed.
Statistical characterization of chemical noise in MALDI TOF MS by wavelet analysis of multiple noise realizations. Shin H, Sampat MP, Bish SF, Koomen JM, Markey MK AMIA Annu Symp Proc. :1092. 2006. View on PubMed.
Proteome analysis of isolated perfused organ effluent as a novel model for protein biomarker discovery. Koomen JM, Wilson CR, Guthrie P, Androlewicz MJ, Kobayashi R, Taegtmeyer H J Proteome Res. 5(1):177-82. doi: 10.1021/pr050170g. January 2006. View on PubMed.
Identification of an inactivating cysteine switch in protein kinase Cepsilon, a rational target for the design of protein kinase Cepsilon-inhibitory cancer therapeutics. Chu F, Koomen JM, Kobayashi R, O'Brian CA Cancer Res. 65(22):10478-85. doi: 10.1158/0008-5472.CAN-05-1989. November 15, 2005. View on PubMed.
Serum amyloid A as a tumor marker in sera of nude mice with orthotopic human pancreatic cancer and in plasma of patients with pancreatic cancer. Yokoi K, Shih LC, Kobayashi R, Koomen J, Hawke D, Li D, Hamilton SR, Abbruzzese JL, Coombes KR, Fidler IJ Int J Oncol. 27(5):1361-9. November 2005. View on PubMed.
Anion template effect on the self-assembly and interconversion of metallacyclophanes. Campos-Fernández CS, Schottel BL, Chifotides HT, Bera JK, Bacsa J, Koomen JM, Russell DH, Dunbar KR J Am Chem Soc. 127(37):12909-23. doi: 10.1021/ja052108q. September 21, 2005. View on PubMed.
Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. Koomen JM, Li D, Xiao LC, Liu TC, Coombes KR, Abbruzzese J, Kobayashi R J Proteome Res. 4(3):972-81. doi: 10.1021/pr050046x. June 2005. View on PubMed.
Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum. Morris JS, Coombes KR, Koomen J, Baggerly KA, Kobayashi R Bioinformatics. 21(9):1764-75. doi: 10.1093/bioinformatics/bti254. May 1, 2005. View on PubMed.
Induction of p21 by p53 following DNA damage inhibits both Cdk4 and Cdk2 activities. He G, Siddik ZH, Huang Z, Wang R, Koomen J, Kobayashi R, Khokhar AR, Kuang J Oncogene. 24(18):2929-43. doi: 10.1038/sj.onc.1208474. April 21, 2005. View on PubMed.
Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins. Koomen JM, Shih LN, Coombes KR, Li D, Xiao LC, Fidler IJ, Abbruzzese JL, Kobayashi R Clin Cancer Res. 11(3):1110-8. February 1, 2005. View on PubMed.
Diagnostic protein discovery using liquid chromatography/mass spectrometry for proteolytic peptide targeting. Koomen JM, Zhao H, Li D, Nasser W, Hawke DH, Abbruzzese JL, Baggerly KA, Kobayashi R Rapid Commun Mass Spectrom. 19(12):1624-36. doi: 10.1002/rcm.1963. 2005. View on PubMed.
Developing an understanding of proteomics: an introduction to biological mass spectrometry. Koomen J, Hawke D, Kobayashi R Cancer Invest. 23(1):47-59. 2005. View on PubMed.
Understanding the characteristics of mass spectrometry data through the use of simulation. Coombes KR, Koomen JM, Baggerly KA, Morris JS, Kobayashi R Cancer Inform. 1:41-52. 2005. View on PubMed.
Binding of DNA purine sites to dirhodium compounds probed by mass spectrometry. Chifotides HT, Koomen JM, Kang M, Tichy SE, Dunbar KR, Russell DH Inorg Chem. 43(20):6177-87. doi: 10.1021/ic040040u. October 4, 2004. View on PubMed.
A circulating ligand for galectin-3 is a haptoglobin-related glycoprotein elevated in individuals with colon cancer. Bresalier RS, Byrd JC, Tessler D, Lebel J, Koomen J, Hawke D, Half E, Liu KF, Mazurek N, Great Lakes-New England Clinical and Epidemiology Center of the Early Detection Research Network Gastroenterology. 127(3):741-8. September 2004. View on PubMed.
Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma. Pusztai L, Gregory BW, Baggerly KA, Peng B, Koomen J, Kuerer HM, Esteva FJ and 8 others Cancer. 100(9):1814-22. doi: 10.1002/cncr.20203. May 1, 2004. View on PubMed.
Lipid/peptide/nucleotide separation with MALDI-ion mobility-TOF MS. Woods AS, Ugarov M, Egan T, Koomen J, Gillig KJ, Fuhrer K, Gonin M, Schultz JA Anal Chem. 76(8):2187-95. doi: 10.1021/ac035376k. April 15, 2004. View on PubMed.
Comparative analyses of the three-dimensional structures and enzymatic properties of alpha, beta, gamma and delta isoforms of Ca2+-calmodulin-dependent protein kinase II. Gaertner TR, Kolodziej SJ, Wang D, Kobayashi R, Koomen JM, Stoops JK, Waxham MN J Biol Chem. 279(13):12484-94. doi: 10.1074/jbc.M313597200. March 26, 2004. View on PubMed.
Diagnostic protein discovery using proteolytic peptide targeting and identification. Koomen JM, Zhao H, Li D, Abbruzzese J, Baggerly K, Kobayashi R Rapid Commun Mass Spectrom. 18(21):2537-48. doi: 10.1002/rcm.1657. 2004. View on PubMed.
Oligonucleotide analysis with MALDI-ion-mobility-TOFMS. Koomen JM, Ruotolo BT, Gillig KJ, McLean JA, Russell DH, Kang M, Dunbar KR, Fuhrer K, Gonin M, Schultz JA Anal Bioanal Chem. 373(7):612-7. doi: 10.1007/s00216-002-1363-2. August 2002. View on PubMed.
Studies on the biosynthesis of phomoidride B (CP-263,114): evidence for a decarboxylative homodimerization pathway. Sulikowski GA, Agnelli F, Spencer P, Koomen JM, Russell DH Org Lett. 4(9):1447-50. May 2, 2002. View on PubMed.
Accurate mass measurement of DNA oligonucleotide ions using high-resolution time-of-flight mass spectrometry. Koomen JM, Russell WK, Tichy SE, Russell DH J Mass Spectrom. 37(4):357-71. doi: 10.1002/jms.312. April 2002. View on PubMed.
A study of peptide-peptide interactions using MALDI ion mobility o-TOF and ESI mass spectrometry. Woods AS, Koomen JM, Ruotolo BT, Gillig KJ, Russel DH, Fuhrer K, Gonin M, Egan TF, Schultz JA J Am Soc Mass Spectrom. 13(2):166-9. doi: 10.1016/S1044-0305(01)00348-8. February 2002. View on PubMed.
Fine-tuning the ring-size of metallacyclophanes: a rational approach to molecular pentagons. Campos-Fernández CS, Clérac R, Koomen JM, Russell DH, Dunbar KR J Am Chem Soc. 123(4):773-4. January 31, 2001. View on PubMed.
Improvement of resolution, mass accuracy, and reproducibility in reflected mode DE-MALDI-TOF analysis of DNA using fast evaporation--overlayer sample preparations. Koomen JM, Russell WK, Hettick JM, Russell DH Anal Chem. 72(16):3860-6. August 15, 2000. View on PubMed.
Ultraviolet/matrix-assisted laser desorption/ionization mass spectrometric characterization of 2,5-dihydroxybenzoic acid-induced reductive hydrogenation of oligonucleotides on cytosine residues. Koomen JM, Russell DH J Mass Spectrom. 35(8):1025-34. doi: 10.1002/1096-9888(200008)35:8<1025::AID-JMS30>3.0.CO;2-9. August 2000. View on PubMed.
Mapping of surrogate markers of cellular components and structures using laser desorption/ionization mass spectrometry. Koomen JM, Stoeckli M, Caprioli RM J Mass Spectrom. 35(2):258-64. doi: 10.1002/(SICI)1096-9888(200002)35:2<258::AID-JMS937>3.0.CO;2-Q. February 2000. View on PubMed.
Mapping catechol-O-methyltransferase in vivo: initial studies with [18F]Ro41-0960. Ding YS, Gatley SJ, Fowler JS, Chen R, Volkow ND, Logan J, Shea CE, Sugano Y, Koomen J Life Sci. 58(3):195-208. 1996. View on PubMed.
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