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Fundamental and Computational Sciences Directorate

Staff information

Thomas Fillmore

Biosystms Dynamics & Simula
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352

PNNL Publications

2017

  • Bryant A, MJ Aldape, CR Bayer, EJ Katahira, L Bond, CD Nicora, TL Fillmore, TRW Clauss, TO Metz, BJM Webb-Robertson, and DL Stevens. 2017. "Effects of delayed NSAID administration after experimental eccentric contraction injury - A cellular and proteomics study." PLoS One 12(12):Article No. e0172486.  doi:10.1371/journal.pone.0172486
  • Kerkhoven EJ, YM Kim, S Wei, CD Nicora, TL Fillmore, SO Purvine, BJM Webb-Robertson, RD Smith, SE Baker, TO Metz, and JB Nielsen. 2017. "Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica." mBio 8(3):Article No. e00857-17.  doi:10.1128/mBio.00857-17
  • Nie S, T Shi, TL Fillmore, AA Schepmoes, HM Brewer, Y Gao, E Song, H Wang, KD Rodland, W Qian, RD Smith, and T Liu. 2017. "Deep-dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues." Analytical Chemistry 89(17):9139-9146.  doi:10.1021/acs.analchem.7b01878
  • Song E, Y Gao, C Wu, T Shi, S Nie, TL Fillmore, AA Schepmoes, MA Gritsenko, W Qian, RD Smith, KD Rodland, and T Liu. 2017. "Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer." Scientific Data 4:170091.  doi:10.1038/sdata.2017.91
  • Wang H, CE Barbieri, J He, Y Gao, T Shi, C Wu, AA Schepmoes, TL Fillmore, SS Chae, D Huang, JM Mosquera, WJ Qian, RD Smith, S Srivastava, J Kagan, DG Camp, II, KD Rodland, M Rubin, and T Liu. 2017. "Quantification of Mutant SPOP Proteins in Prostate Cancer Using Mass Spectrometry-Based Targeted Proteomics." Journal of Translational Medicine 15:Article No. 175.  doi:10.1186/s12967-017-1276-7

2016

  • Guo X, TL Fillmore, Y Gao, and K Tang. 2016. "Capillary Electrophoresis-nanoelectrospray Ionization-selected Reaction Monitoring Mass Spectrometry Via A True Sheathless Metal-coated Emitter Interface For Robust And High Sensitivity Sample Quantification." Analytical Chemistry 88(8):4418-4425.  doi:10.1021/acs.analchem.5b04912
  • Sigdel TK, Y Gao, J He, A Wang, CD Nicora, TL Fillmore, T Shi, BJM Webb-Robertson, RD Smith, W Qian, O Salvatierra, DG Camp, II, and M Sarwal. 2016. "Mining the Human Urine Proteome for Monitoring Renal Transplant Injury ." Kidney International 89(6):1244-1252.  doi:10.1016/j.kint.2015.12.049

2015

  • Chen TC, TL Fillmore, SA Prost, RJ Moore, YM Ibrahim, and RD Smith. 2015. "Orthogonal Injection Ion Funnel Interface Providing Enhanced Performance for Selected Reaction Monitoring-Triple Quadruple Mass Spectrometry." Analytical Chemistry 87(14):7326-7331.  doi:10.1021/acs.analchem.5b01482
  • He J, AA Schepmoes, T Shi, C Wu, TL Fillmore, Y Gao, RD Smith, W Qian, KD Rodland, T Liu, DG Camp, II, A Rastogi, SH Tan, W Yan, AA Mohamed, W Huang, S Banerjee, J Kagan, S Srivastava, D McLeod, S Srivastava, G Petrovics, A Dobi, and A Srinivasan. 2015. "Analytical platform evaluation for quantification of ERG in prostate cancer using protein and mRNA detection methods." Journal of Translational Medicine 13:Article No. 54.  doi:10.1186/s12967-015-0418-z
  • Kebaabetswe LP, AK Haick, MA Gritsenko, TL Fillmore, RK Chu, SO Purvine, BJM Webb-Robertson, MM Matzke, RD Smith, KM Waters, TO Metz, and TA Miura. 2015. "Proteomic Analysis Reveals Down-Regulation of Surfactant Protein B in Murine Type II Pneumocytes Infected with Influenza A Virus." Virology 438:96-107.  doi:10.1016/j.virol.2015.03.045
  • Xu Z, C Wu, F Xie, GW Slysz, N Tolic, ME Monroe, VA Petyuk, SH Payne, GM Fujimoto, RJ Moore, TL Fillmore, AA Schepmoes, D Levine, R Townsend, S Davies, S Li, M Ellis, E Boja, R Rivers, H Rodriguez, KD Rodland, T Liu, and RD Smith. 2015. "Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes." Journal of Proteome Research 14(1):422-433.  doi:10.1021/pr500840w
  • Xu Z, C Wu, F Xie, GW Slysz, N Tolic, ME Monroe, VA Petyuk, SH Payne, GM Fujimoto, RJ Moore, TL Fillmore, AA Schepmoes, D Levine, R Townsend, S Davies, S Li, M Ellis, E Boja, R Rivers, H Rodriguez, KD Rodland, T Liu, and RD Smith. 2015. "Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes." Journal of Proteome Research 14(1):422-433.  doi:10.1021/pr500840w

2014

  • He J, X Sun, T Shi, AA Schepmoes, TL Fillmore, VA Petyuk, F Xie, R Zhao, MA Gritsenko, F Yang, N Kitabayashi, SS Chae, M Rubin, J Siddiqui, J Wei, AM Chinnaiyan, W Qian, RD Smith, J Kagan, S Srivastava, KD Rodland, T Liu, and DG Camp, II. 2014. "Antibody-independent Targeted Quantification of TMPRSS2-ERG Fusion Protein Products in Prostate Cancer." Molecular Oncology 8(7):1169-1180.  doi:10.1016/j.molonc.2014.02.004
  • Hyung SW, PD Piehowski, RJ Moore, DJ Orton, AA Schepmoes, TRW Clauss, RK Chu, TL Fillmore, HM Brewer, T Liu, R Zhao, and RD Smith. 2014. "Microscale Depletion of High Abundance Proteins in Human Biofluids using IgY14 Immunoaffinity Resin: Analysis of Human Plasma and Cerebrospinal Fluid." Analytical and Bioanalytical Chemistry 406(28):7117-7125.  doi:10.1007/s00216-014-8058-3
  • Kronewitter SR, GW Slysz, I Marginean, CD Hagler, BL Lamarche, R Zhao, MY Harris, ME Monroe, CA Polyukh, KL Crowell, TL Fillmore, TS Carlson, DG Camp, II, RJ Moore, SH Payne, GA Anderson, and RD Smith. 2014. "GlyQ-IQ: Glycomics Quintavariate-Informed Quantification with High-Performance Computing and GlycoGrid 4D Visualization." Analytical Chemistry 86(13):6268-6276.  doi:10.1021/ac501492f
  • Shi T, Y Gao, MJ Gaffrey, CD Nicora, TL Fillmore, WB Chrisler, MA Gritsenko, C Wu, J He, KJ Bloodsworth, R Zhao, DG Camp, II, T Liu, KD Rodland, RD Smith, HS Wiley, and W Qian. 2014. "Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells without Affinity Enrichment." Analytical Chemistry 87(2):1103-1110.  doi:10.1021/ac503797x
  • Shi T, Y Gao, SI Quek, TL Fillmore, CD Nicora, D Su, R Zhao, KD Rodland, T Liu, RD Smith, DW Chan, DG Camp, II, AY Liu, and W Qian. 2014. "A highly sensitive targeted mass spectrometric assay for quantification of low-abundance AGR2 in human urine and serum." Journal of Proteome Research 13(2):875-882.  doi:10.1021/pr400912c
  • Wu C, T Shi, JN Brown, J He, Y Gao, TL Fillmore, AK Shukla, RJ Moore, DG Camp, II, KD Rodland, W Qian, T Liu, and RD Smith. 2014. "Expediting SRM assay development for large-scale targeted proteomics experiments." Journal of Proteome Research 13(10):4479-87.  doi:10.1021/pr500500d

2013

  • Shi T, TL Fillmore, Y Gao, R Zhao, J He, AA Schepmoes, CD Nicora, C Wu, JL Chambers, RJ Moore, J Kagan, S Srivastava, AY Liu, KD Rodland, T Liu, DG Camp, II, RD Smith, and W Qian. 2013. "Long-Gradient Separations Coupled with Selected Reaction Monitoring for Highly Sensitive, Large Scale Targeted Protein Quantification in a Single Analysis." Analytical Chemistry 85(19):9196-9203.  doi:10.1021/ac402105s
  • Shi T, X Sun, Y Gao, TL Fillmore, AA Schepmoes, R Zhao, J He, RJ Moore, J Kagan, KD Rodland, T Liu, AY Liu, RD Smith, K Tang, DG Camp, II, and W Qian. 2013. "Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion." Journal of Proteome Research 12(7):3353-3361.  doi:10.1021/pr400178v
  • Zhang Q, TL Fillmore, AA Schepmoes, TRW Clauss, MA Gritsenko, PW Mueller, M Rewers, MA Atkinson, RD Smith, and TO Metz. 2013. "Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes." The Journal of Experimental Medicine 210(1):191-203.  doi:10.1084/jem.20111843

2012

  • Gao X, Q Zhang, D Meng, G Isaac, R Zhao, TL Fillmore, RK Chu, J Zhou, K Tang, Z Hu, RJ Moore, RD Smith, MG Katze, and TO Metz. 2012. "A reversed-phase capillary ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) method for comprehensive top-down/bottom-up lipid profiling." Analytical and Bioanalytical Chemistry 402(9):2923-2933. 
  • Liu T, M Hossain, AA Schepmoes, TL Fillmore, LJ Sokoll, SR Kronewitter, G Izmirlian, T Shi, W Qian, R Leach, IM Thompson, DW Chan, RD Smith, J Kagan, S Srinivastava, KD Rodland, and DG Camp, II. 2012. "Analysis of Serum Total and Free PSA Using Immunoaffinity Depletion Coupled to SRM: Correlation with Clinical Immunoassay Tests." Journal of Proteomics 75(15):4747-4757.  doi:10.1016/j.jprot.2012.01.035
  • Shi T, TL Fillmore, X Sun, R Zhao, AA Schepmoes, M Hossain, F Xie, S Wu, JS Kim, NJ Jones, RJ Moore, L Pasa-Tolic, J Kagan, KD Rodland, T Liu, K Tang, DG Camp, II, RD Smith, and W Qian. 2012. "Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum." Proceedings of the National Academy of Sciences of the United States of America 109(38):15395-15400.  doi:10.1073/pnas.1204366109

2011

  • Kim JS, TL Fillmore, T Liu, EW Robinson, M Hossain, BL Champion, RJ Moore, DG Camp, II, RD Smith, and W Qian. 2011. "18O-Labeled Proteome Reference as Global Internal Standards for Targeted Quantification by Selected Reaction Monitoring-Mass Spectrometry." Molecular & Cellular Proteomics. MCP 10(12):Article No. M110.007302.  doi:10.1074/mcp.M110.007302

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