John <span>M.</span> Koomen
Researcher

John M. Koomen

Academic Rank: Assistant Member

Overview

Our research projects share the common goal of changing the standard of patient assessment and care using mass spectrometry.

Discipline

    • Molecular Oncology
    • Anatomic Pathology
    • Myeloma
    • Melanoma Research Center of Excellence
    • Lung Cancer Center of Excellence
    • Systems Medicine Working Group
    • Chemical Biology and Molecular Medicine Program

Education & Training

    • Texas A&M University, PhD - Chemistry
    • University of Texas at Houston Graduate School of Biomedical Science, MS - Biochemistry
Research

Research in the Koomen Laboratory focuses on analytical chemistry development, elucidation of biological processes, and implementation of clinical assays using proteomics and quantitative mass spectrometry.  Much of this work is performed using multiple reaction monitoring (MRM); three examples are detailed below.  In colon cancer, broad scale proteomics employing relative quantification techniques and gene expression profiles have determined candidate biomarkers related to the Adenomatous Polyposis Coli protein.  Targeted analysis of this panel of proteins coupled with the interrogation of protein expression in relevant signaling pathways, including Wnt, TGF/SMAD, and Notch, in tumors and adjacent normal tissue can be used to select and evaluate candidate biomarkers for predicting patient outcomes.   In multiple myeloma, the same techniques and technologies are being applied in cell lines to develop preclinical models that will provide a molecular basis for rational chemotherapy.  In these experiments, direct drug targets and apoptosis-related proteins are being monitored in parallel with specific signaling pathways, including NFkB.  These data will elucidate mechanisms of drug resistance and provide another method to evaluate combination therapy.   Finally, direct patient assessment is being performed in multiple myeloma using MRM.  Current clinical assays use gel or capillary electrophoresis to measure the antibody secreted by the myeloma, which is used to stage the patients and estimate tumor burden.  Quantitative mass spectrometry should be significantly more sensitive at detecting and quantifying these antibodies.  Improvements in the analytical technique would lead to earlier detection of disease relapse, more rapid intervention with second line therapies, and potentially improved patient outcomes. These projects share the common goal of changing the standard of patient assessment and care using mass spectrometry.    

Publications

  • Chen Y, Britton D, Wood ER, Brantley S, Magliocco A, Pike I, Koomen JM. Quantitative proteomics of breast tumors: Tissue quality assessment to clinical biomarkers. Proteomics. 2017 Mar;17(6). Pubmedid: 28127872.
  • Stewart PA, Fang B, Slebos RJ, Zhang G, Borne AL, Fellows K, Teer JK, Chen YA, Welsh E, Eschrich SA, Haura EB, Koomen JM. Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms. Proteomics. 2017 Mar;17(6). Pubmedid: 28195392.
  • Zhao X, Lwin T, Silva A, Shah B, Tao J, Fang B, Zhang L, Fu K, Bi C, Li J, Jiang H, Meads MB, Jacobson T, Silva M, Distler A, Darville L, Zhang L, Han Y, Rebatchouk D, Di Liberto M, Moscinski LC, Koomen JM, Dalton WS, Shain KH, Wang M, Sotomayor E, Tao J. Unification of de novo and acquired ibrutinib resistance in mantle cell lymphoma. Nat Commun. 2017 Apr;8:14920. Pubmedid: 28416797. Pmcid: PMC5399304.
  • Zhang G, Scarborough H, Kim J, Rozhok AI, Chen YA, Zhang X, Song L, Bai Y, Fang B, Liu RZ, Koomen J, Tan AC, Degregori J, Haura EB. Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors. Sci Signal. 2016 Oct;9(450):rs12. Pubmedid: 27811184. Pmcid: PMC5377910.
  • Guo JP, Shu SK, Esposito NN, Coppola D, Koomen JM, Cheng JQ. IKKϵ phosphorylation of estrogen receptor α Ser-167 and contribution to tamoxifen resistance in breast cancer. J Biol Chem. 2016 Oct;291(43):22857. Pubmedid: 27825095. Pmcid: PMC5077232.
  • Kim JY, Welsh EA, Fang B, Bai Y, Kinose F, Eschrich SA, Koomen JM, Haura EB. Phosphoproteomics Reveals MAPK Inhibitors Enhance MET- and EGFR-Driven AKT Signaling in KRAS-Mutant Lung Cancer. Mol Cancer Res. 2016 Oct;14(10):1019-1029. Pubmedid: 27422710. Pmcid: PMC5065770.
  • Haake SM, Li J, Bai Y, Kinose F, Fang B, Welsh EA, Zent R, Dhillon J, Pow-Sang JM, Chen YA, Koomen JM, Rathmell WK, Fishman M, Haura EB. Tyrosine Kinase Signaling in Clear Cell and Papillary Renal Cell Carcinoma Revealed by Mass Spectrometry-Based Phosphotyrosine Proteomics. Clin Cancer Res. 2016 Nov;22(22):5605-5616. Pubmedid: 27220961. Pmcid: PMC5122466.
  • Meads MB, Fang B, Mathews L, Gemmer J, Nong L, Rosado-Lopez I, Nguyen T, Ring JE, Matsui W, MacLeod AR, Pachter JA, Hazlehurst LA, Koomen JM, Shain KH. Targeting PYK2 mediates microenvironment-specific cell death in multiple myeloma. Oncogene. 2016 May;35(21):2723-2734. Pubmedid: 26387544. Pmcid: PMC4801703.
  • Fedorenko IV, Abel EV, Koomen JM, Fang B, Wood ER, Chen YA, Fisher KJ, Iyengar S, Dahlman KB, Wargo JA, Flaherty KT, Sosman JA, Sondak VK, Messina JL, Gibney GT, Smalley KS. Fibronectin induction abrogates the BRAF inhibitor response of BRAF V600E/PTEN-null melanoma cells. Oncogene. 2016 Mar;35(10):1225-1235. Pubmedid: 26073081. Pmcid: PMC4679729.
  • Chen S, Fisher RC, Signs S, Molina LA, Shenoy AK, Lopez MC, Baker HV, Koomen JM, Chen Y, Gittleman H, Barnholtz-Sloan J, Berg A, Appelman HD, Huang EH. Inhibition of PI3K/Akt/mTOR signaling in PI3KR2-overexpressing colon cancer stem cells reduces tumor growth due to apoptosis. Oncotarget. 2016 Jun. Pubmedid: 27286264.
  • Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura EB. Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer. Proteomes. 2016 Jun;4(2):16. Pubmedid: 28154798. Pmcid: PMC5217344.
  • Jhuraney A, Woods NT, Wright G, Rix L, Kinose F, Kroeger JL, Remily-Wood E, Cress WD, Koomen JM, Brantley SG, Gray JE, Haura EB, Rix U, Monteiro AN. PAXIP1 Potentiates the Combination of WEE1 Inhibitor AZD1775 and Platinum Agents in Lung Cancer. Mol Cancer Ther. 2016 Jul;15(7):1669-1681. Pubmedid: 27196765. Pmcid: PMC4936941.
  • Li J, Fang B, Kinose F, Bai Y, Kim JY, Chen YA, Rix U, Koomen JM, Haura EB. Target Identification in Small Cell Lung Cancer via Integrated Phenotypic Screening and Activity-Based Protein Profiling. Mol Cancer Ther. 2016 Feb;15(2):334-342. Pubmedid: 26772203. Pmcid: PMC4747823.
  • Kuenzi BM, Borne AL, Li J, Haura EB, Eschrich SA, Koomen JM, Rix U, Stewart PA. APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data. J Proteome Res. 2016 Dec;15(12):4747-4754. Pubmedid: 27680298. Pmcid: PMC5231908.
  • Sharma R, Fedorenko I, Spence PT, Sondak VK, Smalley KS, Koomen JM. Activity-Based Protein Profiling Shows Heterogeneous Signaling Adaptations to BRAF Inhibition. J Proteome Res. 2016 Dec;15(12):4476-4489. Pubmedid: 27934295.
  • Knezevic CE, Wright G, Remsing Rix LL, Kim W, Kuenzi BM, Luo Y, Watters JM, Koomen JM, Haura EB, Monteiro AN, Radu C, Lawrence HR, Rix U. Proteome-wide Profiling of Clinical PARP Inhibitors Reveals Compound-Specific Secondary Targets. Cell Chem Biol. 2016 Dec;23(12):1490-1503. Pubmedid: 27866910. Pmcid: PMC5182133.
  • Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura EB. Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer. Proteomes. 2016 Apr;4(2). Pubmedid: 28248226.
  • Stewart PA, Parapatics K, Welsh EA, Müller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB. A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma. PLoS One. 2015 Nov;10(11):e0142162. Pubmedid: 26539827. Pmcid: PMC4634858.
  • Paraiso KH, Thakur MD, Fang B, Koomen JM, Fedorenko IV, John JK, Tsao H, Flaherty KT, Sondak VK, Messina JL, Pasquale EB, Villagra A, Rao UN, Kirkwood JM, Meier F, Sloot S, Gibney GT, Stuart D, Tawbi H, Smalley KS. Ligand-independent EPHA2 signaling drives the adoption of a targeted therapy-mediated metastatic melanoma phenotype. Cancer Discov. 2015 Mar;5(3):264-273. Pubmedid: 25542447. Pmcid: PMC4355213.
  • Schneeberger VE, Ren Y, Luetteke N, Huang Q, Chen L, Lawrence HR, Lawrence NJ, Haura EB, Koomen JM, Coppola D, Wu J. Inhibition of Shp2 suppresses mutant EGFR-induced lung tumors in transgenic mouse model of lung adenocarcinoma. Oncotarget. 2015 Mar;6(8):6191-6202. Pubmedid: 25730908. Pmcid: PMC4467431.
  • Fang B, Hoffman MA, Mirza AS, Mishall KM, Li J, Peterman SM, Smalley KS, Shain KH, Weinberger PM, Wu J, Rix U, Haura EB, Koomen JM. Evaluating kinase ATP uptake and tyrosine phosphorylation using multiplexed quantification of chemically labeled and post-translationally modified peptides. Methods. 2015 Jun;81:41-49. Pubmedid: 25782629. Pmcid: PMC4460980.
  • Sun L, Kokura K, Izumi V, Koomen JM, Seto E, Chen J, Fang J. MPP8 and SIRT1 crosstalk in E-cadherin gene silencing and epithelial-mesenchymal transition. EMBO Rep. 2015 Jun;16(6):689-699. Pubmedid: 25870236. Pmcid: PMC4467853.
  • Fedorenko IV, Fang B, Munko AC, Gibney GT, Koomen JM, Smalley KS. Phosphoproteomic analysis of basal and therapy-induced adaptive signaling networks in BRAF and NRAS mutant melanoma. Proteomics. 2015 Jan;15(2-3):327-339. Pubmedid: 25339196. Pmcid: PMC4389901.
  • Yuan W, Sanda M, Wu J, Koomen J, Goldman R. Quantitative analysis of immunoglobulin subclasses and subclass specific glycosylation by LC-MS-MRM in liver disease. J Proteomics. 2015 Feb;116:24-33. Pubmedid: 25582524. Pmcid: PMC4329072.
  • Damaghi M, Tafreshi NK, Lloyd MC, Sprung R, Estrella V, Wojtkowiak JW, Morse DL, Koomen JM, Bui MM, Gatenby RA, Gillies RJ. Chronic acidosis in the tumour microenvironment selects for overexpression of LAMP2 in the plasma membrane. Nat Commun. 2015 Dec;6:8752. Pubmedid: 26658462. Pmcid: PMC4682176.
  • Peng L, Yuan Z, Li Y, Ling H, Izumi V, Fang B, Fukasawa K, Koomen J, Chen J, Seto E. Ubiquitinated sirtuin 1 (SIRT1) function is modulated during DNA damage-induced cell death and survival. J Biol Chem. 2015 Apr;290(14):8904-8912. Pubmedid: 25670865. Pmcid: PMC4423681.
  • Remily-Wood ER, Benson K, Baz RC, Chen YA, Hussein M, Hartley-Brown MA, Sprung RW, Perez B, Liu RZ, Yoder S, Teer J, Eschrich SA, Koomen JM. Quantification of peptides from immunoglobulin constant and variable regions by LC-MRM MS for assessment of multiple myeloma patients. Proteom Clin Appl. 2014 Oct;8(9-10):783-795. Pubmedid: 24723328. Pmcid: PMC4302417.
  • Fedorenko IV, Fang B, Koomen JM, Gibney GT, Smalley KS. Amuvatinib has cytotoxic effects against NRAS-mutant melanoma but not BRAF-mutant melanoma. Melanoma Res. 2014 Oct;24(5):448-453. Pubmedid: 24950457. Pmcid: PMC4384823.
  • Zheng XQ, Guo JP, Yang H, Kanai M, He LL, Li YY, Koomen JM, Minton S, Gao M, Ren XB, Coppola D, Cheng JQ. Aurora-A is a determinant of tamoxifen sensitivity through phosphorylation of ERα in breast cancer. Oncogene. 2014 Oct;33(42):4985-4996. Pubmedid: 24166501. Pmcid: PMC4002670.
  • Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, H Uumlttenhain R, Koomen JM, Liebler DC, Liu T, Maclean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee J, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics. 2014 Mar;13(3):907-917. Pubmedid: 24443746. Pmcid: PMC3945918.
  • Rebecca VW, Wood ER, Fedorenko IV, Paraiso KH, Haarberg HE, Chen Y, Xiang Y, Sarnaik A, Gibney GT, Sondak VK, Koomen JM, Smalley KS. Evaluating melanoma drug response and therapeutic escape with quantitative proteomics. Mol Cell Proteomics. 2014 Jul;13(7):1844-1854. Pubmedid: 24760959. Pmcid: PMC4083119.
  • Zhang M, Xiang S, Joo HY, Wang L, Williams KA, Liu W, Hu C, Tong D, Haakenson J, Wang C, Zhang S, Pavlovicz RE, Jones A, Schmidt KH, Tang J, Dong H, Shan B, Fang B, Radhakrishnan R, Glazer PM, Matthias P, Koomen J, Seto E, Bepler G, Nicosia SV, Chen J, Li C, Gu L, Li GM, Bai W, Wang H, Zhang X. HDAC6 deacetylates and ubiquitinates MSH2 to maintain proper levels of MutSα. Mol Cell. 2014 Jul;55(1):31-46. Pubmedid: 24882211. Pmcid: PMC4188514.
  • Remsing Rix LL, Kuenzi BM, Luo Y, Remily-Wood E, Kinose F, Wright G, Li J, Koomen JM, Haura EB, Lawrence HR, Rix U. GSK3 alpha and beta are new functionally relevant targets of tivantinib in lung cancer cells. Acs Chem Biol. 2014 Feb;9(2):353-358. Pubmedid: 24215125. Pmcid: PMC3944088.
  • Bai Y, Kim JY, Watters JM, Fang B, Kinose F, Song L, Koomen JM, Teer JK, Fisher K, Chen YA, Rix U, Haura EB. Adaptive responses to dasatinib-treated lung squamous cell cancer cells harboring DDR2 mutations. Cancer Res. 2014 Dec;74(24):7217-7228. Pubmedid: 25348954. Pmcid: PMC4326029.
  • Yoshida T, Zhang G, Smith MA, Lopez AS, Bai Y, Li J, Fang B, Koomen JM, Rawal B, Fisher KJ, Chen YA, Kitano M, Morita Y, Yamaguchi H, Shibata K, Okabe T, Okamoto I, Nakagawa K, Haura EB. Tyrosine phosphoproteomics identifies both codrivers and cotargeting strategies for T790M-related EGFR-TKI resistance in non-small cell lung cancer. Clin Cancer Res. 2014 Aug;20(15):4059-4074. Pubmedid: 24919575. Pmcid: PMC4119578.
  • Koomen JM. Immunoglobulins: expanding the role for mass spectrometry in protein biomarker quantification. Clin Chem. 2014 Aug;60(8):1034-1035. Pubmedid: 24938750. Pmcid: PMC4674789.
  • Yang L, Song T, Chen L, Kabra N, Zheng H, Koomen J, Seto E, Chen J. Regulation of SirT1-nucleomethylin binding by rRNA coordinates ribosome biogenesis with nutrient availability. Mol Cell Biol. 2013 Oct;33(19):3835-3848. Pubmedid: 23897426. Pmcid: PMC3811878.
  • Gebhard AW, Jain P, Nair RR, Emmons MF, Argilagos RF, Koomen JM, McLaughlin ML, Hazlehurst LA. MTI-101 (cyclized HYD1) binds a CD44 containing complex and induces necrotic cell death in multiple myeloma. Mol Cancer Ther. 2013 Nov;12(11):2446-2458. Pubmedid: 24048737. Pmcid: PMC3859963.
  • Williams KA, Zhang M, Xiang S, Hu C, Wu JY, Zhang S, Ryan M, Cox AD, Der CJ, Fang B, Koomen J, Haura E, Bepler G, Nicosia SV, Matthias P, Wang C, Bai W, Zhang X. Extracellular signal-regulated kinase (ERK) phosphorylates histone deacetylase 6 (HDAC6) at serine 1035 to stimulate cell migration. J Biol Chem. 2013 Nov;288(46):33156-33170. Pubmedid: 24089523. Pmcid: PMC3829163.
  • Li J, Bennett K, Stukalov A, Fang B, Zhang G, Yoshida T, Okamoto I, Kim JY, Song L, Bai Y, Qian X, Rawal B, Schell M, Grebien F, Winter G, Rix U, Eschrich S, Colinge J, Koomen J, Superti-Furga G, Haura EB. Perturbation of the mutated EGFR interactome identifies vulnerabilities and resistance mechanisms. Mol Syst Biol. 2013 Nov;9:705. Pubmedid: 24189400. Pmcid: PMC4039310.
  • Ozcan S, Kazi A, Marsilio F, Fang B, Guida WC, Koomen J, Lawrence HR, Sebti SM. Oxadiazole-isopropylamides as potent and noncovalent proteasome inhibitors. J Med Chem. 2013 May;56(10):3783-3805. Pubmedid: 23547706. Pmcid: PMC3774303.
  • Haarberg HE, Paraiso KH, Wood E, Rebecca VW, Sondak VK, Koomen JM, Smalley KS. Inhibition of Wee1, AKT, and CDK4 underlies the efficacy of the HSP90 inhibitor XL888 in an in vivo model of NRAS-mutant melanoma. Mol Cancer Ther. 2013 Jun;12(6):901-912. Pubmedid: 23538902. Pmcid: PMC3683468.
  • Martyniuk CJ, Feswick A, Fang B, Koomen JM, Barber DS, Gavin T, Lopachin RM. Protein targets of acrylamide adduct formation in cultured rat dopaminergic cells. Toxicol Lett. 2013 Jun;219(3):279-287. Pubmedid: 23566896. Pmcid: PMC3707521.
  • Kim JY, Welsh EA, Oguz U, Fang B, Bai Y, Kinose F, Bronk C, Remsing Rix LL, Beg AA, Rix U, Eschrich SA, Koomen JM, Haura EB. Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells. Proc Natl Acad Sci U S A. 2013 Jul;110(30):12414-12419. Pubmedid: 23836654. Pmcid: PMC3725062.
  • Song T, Yang L, Kabra N, Chen L, Koomen J, Haura EB, Chen J. The NAD+ synthesis enzyme nicotinamide mononucleotide adenylyltransferase (NMNAT1) regulates ribosomal RNA transcription. J Biol Chem. 2013 Jul;288(29):20908-20917. Pubmedid: 23737528. Pmcid: PMC3774361.
  • Zheng H, Yang L, Peng L, Izumi V, Koomen J, Seto E, Chen J. hMOF acetylation of DBC1/CCAR2 prevents binding and inhibition of SirT1. Mol Cell Biol. 2013 Dec;33(24):4960-4970. Pubmedid: 24126058. Pmcid: PMC3889553.
  • Pierce Campbell CM, Guan W, Sprung R, Koomen JM, O'Keefe MT, Ingles DJ, Abrahamsen M, Giuliano AR. Quantification of secretory leukocyte protease inhibitor (SLPI) in oral gargle specimens collected using mouthwash. J Immunol Methods. 2013 Dec;400-401:117-121. Pubmedid: 24140751. Pmcid: PMC3990009.
  • Woods NT, Mesquita RD, Sweet M, Carvalho MA, Li X, Liu Y, Nguyen H, Thomas CE, Iversen ES, Marsillac S, Karchin R, Koomen J, Monteiro AN. Charting the landscape of tandem BRCT domain-mediated protein interactions. Sci Signal. 2012 Sep;5(242):rs6. Pubmedid: 22990118. Pmcid: PMC4064718.
  • Mahajan K, Fang B, Koomen JM, Mahajan NP. H2B Tyr37 phosphorylation suppresses expression of replication-dependent core histone genes. Nat Struct Mol Biol. 2012 Sep;19(9):930-937. Pubmedid: 22885324. Pmcid: PMC4533924.
  • Boucher K, Parquet N, Widen R, Shain K, Baz R, Alsina M, Koomen J, Anasetti C, Dalton W, Perez LE. Stemness of B-cell progenitors in multiple myeloma bone marrow. Clin Cancer Res. 2012 Nov;18(22):6155-6168. Pubmedid: 22988056. Pmcid: PMC3500436.
  • Paraiso KH, Haarberg HE, Wood E, Rebecca VW, Chen YA, Xiang Y, Ribas A, Lo RS, Weber JS, Sondak VK, John JK, Sarnaik AA, Koomen JM, Smalley KS. The HSP90 inhibitor XL888 overcomes BRAF inhibitor resistance mediated through diverse mechanisms. Clin Cancer Res. 2012 May;18(9):2502-2514. Pubmedid: 22351686. Pmcid: PMC3398738.
  • Bai Y, Li J, Fang B, Edwards A, Zhang G, Bui M, Eschrich S, Altiok S, Koomen J, Haura EB. Phosphoproteomics identifies driver tyrosine kinases in sarcoma cell lines and tumors. Cancer Res. 2012 May;72(10):2501-2511. Pubmedid: 22461510. Pmcid: PMC4641440.
  • Wilson DS, Fang B, Dalton WS, Meade CD, Koomen JM. An ET-CURE pilot project supporting undergraduate training in cancer research, emerging technology, and health disparities. J Cancer Educ. 2012 Jun;27(3):418-427. Pubmedid: 22528637. Pmcid: PMC3439555.
  • Peng L, Ling H, Yuan Z, Fang B, Bloom G, Fukasawa K, Koomen J, Chen J, Lane WS, Seto E. SIRT1 negatively regulates the activities, functions, and protein levels of hMOF and TIP60. Mol Cell Biol. 2012 Jul;32(14):2823-2836. Pubmedid: 22586264. Pmcid: PMC3416197.
  • An Z, Chen Y, Koomen JM, Merkler DJ. A mass spectrometry-based method to screen for α-amidated peptides. Proteomics. 2012 Jan;12(2):173-182. Pubmedid: 22106059. Pmcid: PMC3517110.
  • Xiang Y, Koomen JM. Evaluation of direct infusion-multiple reaction monitoring mass spectrometry for quantification of heat shock proteins. Anal Chem. 2012 Feb;84(4):1981-1986. Pubmedid: 22293045. Pmcid: PMC3332078.
  • Remily-Wood ER, Koomen JM. Evaluation of protein quantification using standard peptides containing single conservative amino acid replacements. J Mass Spectrom. 2012 Feb;47(2):188-194. Pubmedid: 22359328. Pmcid: PMC3465614.
  • John JK, Paraiso KH, Rebecca VW, Cantini LP, Abel EV, Pagano N, Meggers E, Mathew R, Krepler C, Izumi V, Fang B, Koomen JM, Messina JL, Herlyn M, Smalley KS. GSK3β inhibition blocks melanoma cell/host interactions by downregulating N-cadherin expression and decreasing FAK phosphorylation. J Invest Dermatol. 2012 Dec;132(12):2818-2827. Pubmedid: 22810307. Pmcid: PMC3479306.
  • Xiang Y, Remily-Wood ER, Oliveira V, Yarde D, He L, Cheng JQ, Mathews L, Boucher K, Cubitt C, Perez L, Gauthier TJ, Eschrich SA, Shain KH, Dalton WS, Hazlehurst L, Koomen JM. Monitoring a nuclear factor-κB signature of drug resistance in multiple myeloma. Mol Cell Proteomics. 2011 Nov;10(11):M110.005520. Pubmedid: 21846842. Pmcid: PMC3226396.
  • Chang Y, Sun L, Kokura K, Horton JR, Fukuda M, Espejo A, Izumi V, Koomen JM, Bedford MT, Zhang X, Shinkai Y, Fang J, Cheng X. MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a. Nat Commun. 2011 Nov;2:533. Pubmedid: 22086334. Pmcid: PMC3286832.
  • Wong PG, Winter SL, Zaika E, Cao TV, Oguz U, Koomen JM, Hamlin JL, Alexandrow MG. Cdc45 limits replicon usage from a low density of preRCs in mammalian cells. PLoS One. 2011 Mar;6(3):e17533. Pubmedid: 21390258. Pmcid: PMC3046982.
  • Zhang G, Fang B, Liu RZ, Lin H, Kinose F, Bai Y, Oguz U, Remily-Wood ER, Li J, Altiok S, Eschrich S, Koomen J, Haura EB. Mass spectrometry mapping of epidermal growth factor receptor phosphorylation related to oncogenic mutations and tyrosine kinase inhibitor sensitivity. J Proteome Res. 2011 Jan;10(1):305-319. Pubmedid: 21080693. Pmcid: PMC3050523.
  • Peng L, Yuan Z, Ling H, Fukasawa K, Robertson K, Olashaw N, Koomen J, Chen J, Lane WS, Seto E. SIRT1 deacetylates the DNA methyltransferase 1 (DNMT1) protein and alters its activities. Mol Cell Biol. 2011 Dec;31(23):4720-4734. Pubmedid: 21947282. Pmcid: PMC3232929.
  • Martyniuk CJ, Fang B, Koomen JM, Gavin T, Zhang L, Barber DS, Lopachin RM. Molecular mechanism of glyceraldehyde-3-phosphate dehydrogenase inactivation by α,β-unsaturated carbonyl derivatives. Chem Res Toxicol. 2011 Dec;24(12):2302-2311. Pubmedid: 22084934. Pmcid: PMC3243798.
  • Remily-Wood ER, Liu RZ, Xiang Y, Chen Y, Thomas CE, Rajyaguru N, Kaufman LM, Ochoa JE, Hazlehurst L, Pinilla-Ibarz J, Lancet J, Zhang G, Haura E, Shibata D, Yeatman T, Smalley KS, Dalton WS, Huang E, Scott E, Bloom GC, Eschrich SA, Koomen JM. A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. Proteom Clin Appl. 2011 Aug;5(7-8):383-396. Pubmedid: 21656910. Pmcid: PMC3530891.
  • Koomen JM, Smalley KS. Using quantitative proteomic analysis to understand genotype specific intrinsic drug resistance in melanoma. Oncotarget. 2011 Apr;2(4):329-335. Pubmedid: 21505227. Pmcid: PMC3248164.
  • Paraiso KH, Xiang Y, Rebecca VW, Abel EV, Chen YA, Munko AC, Wood E, Fedorenko IV, Sondak VK, Anderson AR, Ribas A, Palma MD, Nathanson KL, Koomen JM, Messina JL, Smalley KS. PTEN loss confers BRAF inhibitor resistance to melanoma cells through the suppression of BIM expression. Cancer Res. 2011 Apr;71(7):2750-2760. Pubmedid: 21317224. Pmcid: PMC3070772.
  • Fang B, Haura EB, Smalley KS, Eschrich SA, Koomen JM. Methods for investigation of targeted kinase inhibitor therapy using chemical proteomics and phosphorylation profiling. Biochem Pharmacol. 2010 Sep;80(5):739-747. Pubmedid: 20361944. Pmcid: PMC2995952.
  • Ren Y, Chen Z, Chen L, Fang B, Win-Piazza H, Haura E, Koomen JM, Wu J. Critical role of Shp2 in tumor growth involving regulation of c-Myc. Genes Cancer. 2010 Oct;1(10):994-1007. Pubmedid: 21442024. Pmcid: PMC3063420.
  • Machida K, Eschrich S, Li J, Bai Y, Koomen J, Mayer BJ, Haura EB. Characterizing tyrosine phosphorylation signaling in lung cancer using SH2 profiling. PLoS One. 2010 Oct;5(10):e13470. Pubmedid: 20976048. Pmcid: PMC2957407.
  • Mahajan K, Coppola D, Challa S, Fang B, Chen YA, Zhu W, Lopez AS, Koomen J, Engelman RW, Rivera C, Muraoka-Cook RS, Cheng JQ, Schönbrunn E, Sebti SM, Earp HS, Mahajan NP. Ack1 mediated AKT/PKB tyrosine 176 phosphorylation regulates its activation. PLoS One. 2010 Mar;5(3):e9646. Pubmedid: 20333297. Pmcid: PMC2841635.
  • Shin H, Sampat MP, Koomen JM, Markey MK. Wavelet-Based Adaptive Denoising and Baseline Correction for MALDI TOF MS. OMICS. 2010 Jun;14(3):283-295. Pubmedid: 20455751.
  • Kahali S, Sarcar B, Fang B, Williams ES, Koomen JM, Tofilon PJ, Chinnaiyan P. Activation of the unfolded protein response contributes toward the antitumor activity of vorinostat. Neoplasia. 2010 Jan;12(1):80-86. Pubmedid: 20072656. Pmcid: PMC2805886.
  • Guo JP, Shu SK, Esposito NN, Coppola D, Koomen JM, Cheng JQ. IKKepsilon phosphorylation of estrogen receptor alpha Ser-167 and contribution to tamoxifen resistance in breast cancer. J Biol Chem. 2010 Feb;285(6):3676-3684. Pubmedid: 19940156. Pmcid: PMC2823508.
  • Chen Y, Gruidl M, Remily-Wood E, Liu RZ, Eschrich S, Lloyd M, Nasir A, Bui MM, Huang E, Shibata D, Yeatman T, Koomen JM. Quantification of beta-catenin signaling components in colon cancer cell lines, tissue sections, and microdissected tumor cells using reaction monitoring mass spectrometry. J Proteome Res. 2010 Aug;9(8):4215-4227. Pubmedid: 20590165. Pmcid: PMC2924816.
  • Chen L, Li Z, Zwolinska AK, Smith MA, Cross B, Koomen J, Yuan ZM, Jenuwein T, Marine JC, Wright KL, Chen J. MDM2 recruitment of lysine methyltransferases regulates p53 transcriptional output. Embo J. 2010 Aug;29(15):2538-2552. Pubmedid: 20588255. Pmcid: PMC2928696.
  • Thomas CE, Sexton W, Benson K, Sutphen R, Koomen J. Urine collection and processing for protein biomarker discovery and quantification. Cancer Epidemiol Biomarkers Prev. 2010 Apr;19(4):953-959. Pubmedid: 20332277. Pmcid: PMC2852495.
  • Li J, Rix U, Fang B, Bai Y, Edwards A, Colinge J, Bennett KL, Gao J, Song L, Eschrich S, Superti-Furga G, Koomen J, Haura EB. A chemical and phosphoproteomic characterization of dasatinib action in lung cancer. Nat Chem Biol. 2010 Apr;6(4):291-299. Pubmedid: 20190765. Pmcid: PMC2842457.
  • Remily-Wood E, Dirscherl H, Koomen JM. Acid hydrolysis of proteins in matrix assisted laser desorption ionization matrices. J Am Soc Mass Spectrom. 2009 Nov;20(11):2106-2115. Pubmedid: 19679491.
  • Lu D, Liu RZ, Izumi V, Fenstermacher D, Haura EB, Koomen J, Eschrich SA. IPEP: an in silico tool to examine proteolytic peptides for mass spectrometry. Bioinformatics. 2009 Jan;24(23):2801-2802. Pubmedid: 18842605.
  • Koomen JM, Haura EB, Bepler G, Sutphen R, Remily-Wood ER, Benson K, Hussein M, Hazlehurst LA, Yeatman TJ, Hildreth LT, Sellers TA, Jacobsen PB, Fenstermacher DA, Dalton WS. Proteomic contributions to personalized cancer care. Mol Cell Proteomics. 2008 Oct;7(10):1780-1794. Pubmedid: 18664563. Pmcid: PMC2559938.
  • Shin H, Mutlu M, Koomen JM, Markey MK. Parametric power spectral density analysis of noise from instrumentation in MALDI TOF mass spectrometry. Cancer Inform. 2007 Sep;3:219-230. Pubmedid: 19455245. Pmcid: PMC2675828.
  • Ohshiro K, Rosenthal D, Koomen J, Streckfus C, Chambers M, Kobayashi R, El-Naggar A. Pre-analytic saliva processing affect proteomic results and biomarker screening of head and neck squamous carcinoma. Int J Oncol. 2007 Mar;30(3):743-749. Pubmedid: 17273777.
  • Zhang X, Yuan Z, Zhang Y, Yong S, Salas-Burgos A, Koomen J, Olashaw N, Parsons JT, Yang XJ, Dent SR, Yao TP, Lane WS, Seto E. HDAC6 modulates cell motility by altering the acetylation level of cortactin. Mol Cell. 2007 Jul;27(2):197-213. Pubmedid: 17643370. Pmcid: PMC2684874.
  • Pan S, Wang R, Zhou X, He G, Koomen J, Kobayashi R, Sun L, Corvera J, Gallick GE, Kuang J. Involvement of the conserved adaptor protein Alix in actin cytoskeleton assembly. J Biol Chem. 2006 Nov;281(45):34640-34650. Pubmedid: 16966331.
  • Koomen J, Wilson C, Guthrie P, Androlewicz M, Kobayashi R, Taegtmeyer H. Proteome analysis of isolated perfused organ effluent as a novel model for protein biomarker discovery. J Proteome Res. 2006 Jan;5(1):177-182. Pubmedid: 16396509.
  • Coussot G, Hawke D, Mularz A, Koomen J, Kobayashi R. A method for the isolation of blocked N-terminal peptides. Anal Biochem. 2006 Feb;361(2):302-4. Pubmedid: 17188638.
  • Shin H, Sampat M, Bish S, Koomen J, Markey M. Statistical characterization of chemical noise in MALDI TOF MS by wavelet analysis of multiple noise realizations. Amia Annu Symp Proc. 2006;1092. Pubmedid: 17238711. Pmcid: PMC1839299.
  • Campos-Fernandez C, Schottel B, Chifotides H, Bera J, Bacsa J, Koomen JM, Russell D, Dunbar K. Anion template effect on the self-assembly and interconversion of metallacyclophanes. J Am Chem Soc. 2005 Oct;127(37):12909-12923. Pubmedid: 16159285.
  • Chu F, Koomen JM, Kobayashi R, O'Brian CA. Identification of an inactivating cysteine switch in protein kinase Cepsilon, a rational target for the design of protein kinase Cepsilon-inhibitory cancer therapeutics. Cancer Res. 2005 Nov;65(22):10478-10485. Pubmedid: 16288040.
  • Yokoi K, Shih LC, Kobayashi R, Koomen J, Hawke D, Li D, Hamilton SR, Abbruzzese JL, Coombes KR, Fidler IJ. 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. Int J Oncol. 2005 Nov;27(5):1361-1369. Pubmedid: 16211233.
  • 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 May;21(9):1764-1775. Pubmedid: 15673564.
  • Koomen J, Shih L, Coombes K, Li D, Xiao L, Fidler I, Abbruzzese J, Kobayashi R. Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins. Clin Cancer Res. 2005 Feb;11(3):1110-1118. Pubmedid: 15709178.
  • 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 Apr;24(18):2929-2943. Pubmedid: 15735718.
  • Coombes KR, Koomen JM, Baggerly KA, Morris JS, Kobayashi R. Understanding the characteristics of mass spectrometry data through the use of simulation. Cancer Inform. 2005;1:41-52. Pubmedid: 19305631. Pmcid: PMC2657656.
  • Koomen J, Zhao H, Li D, Nasser W, Hawke D, Abbruzzese J, Baggerly K, Kobayashi R. Diagnostic protein discovery using liquid chromatography/mass spectrometry for proteolytic peptide targeting. Rapid Commun Mass Spectrom. 2005;19(12):1624-1636. Pubmedid: 15915451.
  • Bresalier RS, Byrd JC, Tessler D, Lebel J, Koomen J, Hawke D, Half E, Liu KF, Mazurek N. A circulating ligand for galectin-3 is a haptoglobin-related glycoprotein elevated in individuals with colon cancer. Gastroenterology. 2004 Sep;127(3):741-748. Pubmedid: 15362030.
  • Chifotides H, Koomen J, Kang M, Tichy S, Dunbar K, Russell D. Binding of DNA purine sites to dirhodium compounds probed by mass spectrometry. Inorg Chem. 2004 Oct;43(20):6177-6187. Pubmedid: 15446862.
  • Pusztai L, Gregory BW, Baggerly KA, Peng B, Koomen J, Kuerer HM, Esteva FJ, Symmans WF, Wagner P, Hortobagyi GN, Laronga C, Semmes OJ, Wright GL, Drake RR, Vlahou A. Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma. Cancer. 2004 May;100(9):1814-1822. Pubmedid: 15112261.
  • Gaertner T, Kolodziej S, Wang D, Kobayashi R, Koomen J, Stoops J, WaxhamMN. Comparative analyses of the three-dimensional structures and enzymatic properties of alpha, beta, gamma and delta isoforms of Ca2+-calmodulin-dependent protein kinase II. J Biol Chem. 2004 Mar;279(13):12484-12494. Pubmedid: 14722083.
  • Woods A, Ugarov M, Egan T, Koomen J, Gillig K, Fuhrer K, Gonin M, SchultzJA. Lipid/peptide/nucleotide separation with MALDI-ion mobility-TOF MS. Anal Chem. 2004 Apr;76(8):2187-2195. Pubmedid: 15080727.
  • Koomen J, Zhao H, Li D, Abbruzzese J, Baggerly K, Kobayashi R. Diagnostic protein discovery using proteolytic peptide targeting and identification. Rapid Commun Mass Spectrom. 2004;18(21):2537-2548. Pubmedid: 15468157.
  • Woods AS, Koomen JM, Ruotolo BT, Gillig KJ, Russel DH, Fuhrer K, Gonin M, Egan TF, Schultz JA. A study of peptide-peptide interactions using MALDI ion mobility o-TOF and ESI mass spectrometry. J Am Soc Mass Spectrom. 2002 Feb;13(2):166-169. Pubmedid: 11838019.
  • Koomen J, Ruotolo B, Gillig K, McLean J, Russell D, Kang M, Dunbar K, Fuhrer K, Gonin M, Schultz J. Oligonucleotide analysis with MALDI-ion-mobility-TOFMS. Anal Bioanal Chem. 2002 Aug;373(7):612-617. Pubmedid: 12185573.
  • Koomen J, Russell W, Tichy S, Russell D. Accurate mass measurement of DNA oligonucleotide ions using high-resolution time-of-flight mass spectrometry. J Mass Spectrom. 2002;37(4):357-371. Pubmedid: 11948842.
  • Sulikowski G, Agnelli F, Spencer P, Koomen J, Russell D. Studies on the biosynthesis of phomoidride B (CP-263,114): evidence for a decarboxylative homodimerization pathway. Org Lett. 2002;4(9):1447-1450. Pubmedid: 11975600.
  • Campos-Fernandez C, Clerac R, Koomen J, Russell D, Dunbar K. Fine-tuning the ring-size of metallacyclophanes: a rational approach to molecular pentagons. J Am Chem Soc. 2001;123(4):773-774. Pubmedid: 11456607.
  • Botos I, Meyer E, Nguyen M, Swanson S, Koomen J, Russell D, Meyer E. The structure of an insect chymotrypsin. J Mol Biol. 2000 May;298(5):895-901. Pubmedid: 10801356.
  • Koomen JM, Russell DH. Ultraviolet/matrix-assisted laser desorption/ionization mass spectrometric characterization of 2,5-dihydroxybenzoic acid-induced reductive hydrogenation of oligonucleotides on cytosine residues. J Mass Spectrom. 2000 Aug;35(8):1025-1034. Pubmedid: 10973002.
  • Julicher RH, Sterrenberg L, Koomen JM, Bast A, Noordhoek J. Evidence for lipid peroxidation during the calcium paradox in vitamin E-deficient rat heart. Naunyn Schmiedebergs Arch Pharmacol. 1984 May;326(1):87-89. Pubmedid: 6472488.
  • Koomen JM, Schevers JA, Noordhoek J. Myocardial recovery from global ischemia and reperfusion: effects of pre- and/or post-ischemic perfusion with low-Ca2+. J Mol Cell Cardiol. 1983 Jun;15(6):383-392. Pubmedid: 6876187.
  • Koomen J, Li D, Xiao L, Liu T, Coombes K, Abbruzzese J, Kobayashi R. Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. J Proteome Res. 4(3):972-981. Pubmedid: 15952745.