Thomas Fillmore
Chemist
Thomas Fillmore is an analytical chemist with the Biomolecular Pathways team. He has an extensive background in gas chromatography and high-performance liquid chromatography, with several years of experience in mass spectrometry (MS). Before working for PNNL and EMSL Fillmore’s work required him to maintain and utilize a wide variety of instrumentation, create, and validate analytical methods and protocols for Food and Drug Administration and Environmental Protection Agency approval, and review client reports before regulatory release.
Since coming to PNNL and EMSL in 2009, Fillmore has increased his working and theoretical knowledge of mass spectrometry. He is a point of contact for EMSL users, contributes to experimental design, and coordinates the use of and maintains the triple quad instrumentation. He also works with senior scientists on instrument development and provides high-quality data on time.
Education
BS in Chemistry, Montana State University
Awards and Recognition
Outstanding Performance Award, PNNL (2010, 2011, 2012, and 2013)
Publications
2020
Gao Y., Y. Wang, Y. Chen, H. Wang, D. Young, T. Shi, and Y. Song, et al. 2020. "Proteomic Tissue-based Classifier for Early Prediction of Prostate Cancer Progression." Cancers 12, no. 5:1268. PNNL-SA-149705. doi:10.3390/cancers12051268
Lee J., T. Shi, V.A. Petyuk, A.A. Schepmoes, T.L. Fillmore, Y. Wang, and W.A. Cardoni, et al. 2020. "Detection of head and neck cancer based on longitudinal changes in serum protein abundance." Cancer Epidemiology, Biomarkers and Prevention 29, no. 8:1665-1672. PNNL-ACT-SA-10471. doi:10.1158/1055-9965.EPI-20-0192
2019
Dou M., C. Tsai, P.D. Piehowski, Y. Wang, T.L. Fillmore, R. Zhao, and R.J. Moore, et al. 2019. "Automated Nanoflow Two-Dimensional Reversed-Phase Liquid Chromatography System Enables In-Depth Proteome and Phosphoproteome Profiling of Nanoscale Samples." Analytical Chemistry 91, no. 15:9707-9715. PNNL-SA-141437. doi:10.1021/acs.analchem.9b01248
Gibbons B.C., T.L. Fillmore, Y. Gao, R.J. Moore, T. Liu, E.S. Nakayasu, and T.O. Metz, et al. 2019. "Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards." Journal of Proteome Research 18, no. 2:694-699. PNNL-SA-137457. doi:10.1021/acs.jproteome.8b00688
Moghieb A.M., L. Tesfay, S. Nie, M.A. Gritsenko, T.L. Fillmore, J.M. Jacobs, and R.D. Smith, et al. 2019. "A Targeted Mass Spectrometric Assay for Reliable Sensitive Hepcidin Quantification." Scientific Reports 9, no. 1:Article No. 7264. PNNL-SA-138022. doi:10.1038/s41598-019-43756-9
Nagarajan A., M. Zhou, A.Y. Nguyen, M.L. Liberton, K. Kedia, T. Shi, and P.D. Piehowski, et al. 2019. "Proteomic insights into phycobilisome degradation, a selective and tightly controlled process in the fast growing cyanobacterium Synechococcus elongatus UTEX 2973." Biomolecules 9, no. 8:Article Number 374. PNNL-SA-146394. doi:10.3390/biom9080374
Zhang P., M.J. Gaffrey, Y. Zhu, W.B. Chrisler, T.L. Fillmore, L. Yi, and C.D. Nicora, et al. 2019. "Carrier-assisted single-tube processing approach for targeted proteomics analysis of low numbers of mammalian cells." Analytical Chemistry 91, no. 2:1441-1451. PNNL-SA-138130. doi:10.1021/acs.analchem.8b04258
2018
Callister S.J., T.L. Fillmore, C.D. Nicora, J.B. Shaw, S.O. Purvine, D.J. Orton, and R.A. White, et al. 2018. "Addressing the challenge of soil metaproteome complexity by improving metaproteome depth of coverage Through two-dimensional liquid chromatography." Soil Biology and Biochemistry 125. PNNL-SA-131999. doi:10.1016/j.soilbio.2018.07.018
Gargano A., J.B. Shaw, M. Zhou, C.S. Wilkins, T.L. Fillmore, R.J. Moore, and G.W. Somsen, et al. 2018. "Increasing the Separation Capacity of Intact Histone Proteoforms Chromatography Coupling Online Weak Cation Exchange-HILIC to Reversed Phase LC UVPD-HRMS." Journal of Proteome Research 17, no. 11:3791-3800. PNNL-SA-138847. doi:10.1021/acs.jproteome.8b00458
Orton D.J., M.M. Tfaily, R.J. Moore, B.L. Lamarche, X. Zheng, T.L. Fillmore, and R.K. Chu, et al. 2018. "A Customizable Flow Injection System for Automated, High Throughput and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements." Analytical Chemistry 90, no. 1:737-744. PNNL-SA-128111. doi:10.1021/acs.analchem.7b02986
Piehowski P.D., V.A. Petyuk, R.L. Sontag, M.A. Gritsenko, K.K. Weitz, T.L. Fillmore, and J.S. Moon, et al. 2018. "Residual tissue repositories as a resource for population-based cancer proteomic studies." Clinical Proteomics 15. PNNL-SA-130920. doi:10.1186/s12014-018-9202-4
Shi T., M.J. Gaffrey, T.L. Fillmore, C.D. Nicora, L. Yi, P. Zhang, and A.K. Shukla, et al. 2018. "Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells." Communications Biology 1, no. 1:Article No. 103. PNNL-SA-130600. doi:10.1038/s42003-018-0107-6
Yi L., T. Shi, M.A. Gritsenko, C. Chan, T.L. Fillmore, B.M. Hess, and A.C. Swensen, et al. 2018. "Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway." Analytical Chemistry 90, no. 8:5256-5263. PNNL-SA-131519. doi:10.1021/acs.analchem.8b00071
Yu L., V.A. Petyuk, C. Gaiteri, S. Mostafavi, T. Young-Pearse, R.C. Shah, and A. Buchman, et al. 2018. "Targeted Brain Proteomics Uncover Multiple Pathways to Alzheimer's Dementia." Annals of Neurology 84, no. 1:78-88. PNNL-SA-136156. doi:10.1002/ana.25266
2017
Bryant A., M.J. Aldape, C.R. Bayer, E.J. Katahira, L. Bond, C.D. Nicora, and T.L. Fillmore, et al. 2017. "Effects of delayed NSAID administration after experimental eccentric contraction injury - A cellular and proteomics study." PLoS One 12, no. 12:Article No. e0172486. PNNL-SA-112551. doi:10.1371/journal.pone.0172486
Kerkhoven E.J., Y. Kim, S. Wei, C.D. Nicora, T.L. Fillmore, S.O. Purvine, and B.M. Webb-Robertson, et al. 2017. "Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica." mBio 8, no. 3:Article No. e00857-17. PNNL-SA-122829. doi:10.1128/mBio.00857-17
Nie S., T. Shi, T.L. Fillmore, A.A. Schepmoes, H.M. Brewer, Y. Gao, and E. Song, et al. 2017. "Deep-dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues." Analytical Chemistry 89, no. 17:9139-9146. PNNL-SA-126297. doi:10.1021/acs.analchem.7b01878
Shi T., S. Quek, Y. Gao, C.D. Nicora, S. Nie, T.L. Fillmore, and T. Liu, et al. 2017. "Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins." Oncotarget 8, no. 60:101887-101898. PNNL-SA-128413. doi:10.18632/oncotarget.21710
Song E., Y. Gao, C. Wu, T. Shi, S. Nie, T.L. Fillmore, and A.A. Schepmoes, et al. 2017. "Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer." Scientific Data. PNNL-SA-122408. doi:10.1038/sdata.2017.91
2016
Guo X., T.L. 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, no. 8:4418-4425. PNNL-SA-115236. doi:10.1021/acs.analchem.5b04912
Sigdel T.K., Y. Gao, J. He, A. Wang, C.D. Nicora, T.L. Fillmore, and T. Shi, et al. 2016. "Mining the Human Urine Proteome for Monitoring Renal Transplant Injury." Kidney International 89, no. 6:1244-1252. PNNL-SA-115293. doi:10.1016/j.kint.2015.12.049
Tolic N., M.M. Tfaily, Y. Shen, R.K. Chu, T.L. Fillmore, R. Zhao, and K.J. Bloodsworth, et al. 2016. "Soil Organic Matter (SOM): Mass Spectrometry Data Analysis." In Encyclopedia of Soil Science, Third Edition, edited by R Lal. Boca Raton, Florida:CRC Press. PNNL-SA-117244. doi:10.1081/E-ESS3-120053757
2015
Chen T., T.L. Fillmore, S.A. Prost, R.J. Moore, Y.M. Ibrahim, and R.D. Smith. 2015. "Orthogonal Injection Ion Funnel Interface Providing Enhanced Performance for Selected Reaction Monitoring-Triple Quadruple Mass Spectrometry." Analytical Chemistry 87, no. 14:7326-7331. PNNL-SA-109430. doi:10.1021/acs.analchem.5b01482
He J., A.A. Schepmoes, T. Shi, C. Wu, T.L. Fillmore, Y. Gao, and R.D. Smith, et al. 2015. "Analytical platform evaluation for quantification of ERG in prostate cancer using protein and mRNA detection methods." Journal of Translational Medicine 13. PNNL-SA-107827. doi:10.1186/s12967-015-0418-z
Kebaabetswe L.P., A.K. Haick, M.A. Gritsenko, T.L. Fillmore, R.K. Chu, S.O. Purvine, and B.M. Webb-Robertson, et al. 2015. "Proteomic Analysis Reveals Down-Regulation of Surfactant Protein B in Murine Type II Pneumocytes Infected with Influenza A Virus." Virology 438. PNWD-SA-10439. doi:10.1016/j.virol.2015.03.045
Xu Z., C. Wu, F. Xie, G.W. Slysz, N. Tolic, M.E. Monroe, and V.A. Petyuk, et al. 2015. "Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes." Journal of Proteome Research 14, no. 1:422-433. PNNL-SA-103951. doi:10.1021/pr500840w
2014
He J., X. Sun, T. Shi, A.A. Schepmoes, T.L. Fillmore, V.A. Petyuk, and F. Xie, et al. 2014. "Antibody-independent Targeted Quantification of TMPRSS2-ERG Fusion Protein Products in Prostate Cancer." Molecular Oncology 8, no. 7:1169-1180. PNNL-SA-97917. doi:10.1016/j.molonc.2014.02.004
Hyung S., P.D. Piehowski, R.J. Moore, D.J. Orton, A.A. Schepmoes, T.R. Clauss, and R.K. Chu, et al. 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, no. 28:7117-7125. PNNL-SA-92758. doi:10.1007/s00216-014-8058-3
Kronewitter S.R., G.W. Slysz, I. Marginean, C.D. Hagler, B.L. Lamarche, R. Zhao, and M.Y. Harris, et al. 2014. "GlyQ-IQ: Glycomics Quintavariate-Informed Quantification with High-Performance Computing and GlycoGrid 4D Visualization." Analytical Chemistry 86, no. 13:6268-6276. PNNL-SA-100272. doi:10.1021/ac501492f
Shi T., Y. Gao, M.J. Gaffrey, C.D. Nicora, T.L. Fillmore, W.B. Chrisler, and M.A. Gritsenko, et al. 2014. "Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells without Affinity Enrichment." Analytical Chemistry 87, no. 2:1103-1110. PNNL-SA-103421. doi:10.1021/ac503797x
Shi T., Y. Gao, S. Quek, T.L. Fillmore, C.D. Nicora, D. Su, and R. Zhao, et al. 2014. "A highly sensitive targeted mass spectrometric assay for quantification of low-abundance AGR2 in human urine and serum." Journal of Proteome Research 13, no. 2:875-882. PNWD-SA-10119. doi:10.1021/pr400912c
Wu C., T. Shi, J.N. Brown, J. He, Y. Gao, T.L. Fillmore, and A.K. Shukla, et al. 2014. "Expediting SRM assay development for large-scale targeted proteomics experiments." Journal of Proteome Research 13, no. 10:4479-87. PNNL-SA-102906. doi:10.1021/pr500500d
2013
Shi T., T.L. Fillmore, Y. Gao, R. Zhao, J. He, A.A. Schepmoes, and C.D. Nicora, et al. 2013. "Long-Gradient Separations Coupled with Selected Reaction Monitoring for Highly Sensitive, Large Scale Targeted Protein Quantification in a Single Analysis." Analytical Chemistry 85, no. 19:9196-9203. PNNL-SA-96700. doi:10.1021/ac402105s
Shi T., X. Sun, Y. Gao, T.L. Fillmore, A.A. Schepmoes, R. Zhao, and J. He, et al. 2013. "Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion." Journal of Proteome Research 12, no. 7:3353-3361. PNNL-SA-92544. doi:10.1021/pr400178v
Zhang Q., T.L. Fillmore, A.A. Schepmoes, T.R. Clauss, M.A. Gritsenko, P.W. Mueller, and M. Rewers, et al. 2013. "Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes." The Journal of Experimental Medicine 210, no. 1:191-203. PNNL-SA-89853. doi:10.1084/jem.20111843
2012
Gao X., Q. Zhang, D. Meng, G. Isaac, R. Zhao, T.L. Fillmore, and R.K. Chu, et al. 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, no. 9:2923-2933. PNWD-SA-9553.
Liu T., M. Hossain, A.A. Schepmoes, T.L. Fillmore, L.J. Sokoll, S.R. Kronewitter, and G. Izmirlian, et al. 2012. "Analysis of Serum Total and Free PSA Using Immunoaffinity Depletion Coupled to SRM: Correlation with Clinical Immunoassay Tests." Journal of Proteomics 75, no. 15:4747-4757. PNNL-SA-83777. doi:10.1016/j.jprot.2012.01.035
Shi T., T.L. Fillmore, X. Sun, R. Zhao, A.A. Schepmoes, M. Hossain, and F. Xie, et al. 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, no. 38:15395-15400. PNNL-SA-83776. doi:10.1073/pnas.1204366109
2011
Kim J., T.L. Fillmore, T. Liu, E.W. Robinson, M. Hossain, B.L. Champion, and R.J. Moore, et al. 2011. "18O-Labeled Proteome Reference as Global Internal Standards for Targeted Quantification by Selected Reaction Monitoring-Mass Spectrometry." Molecular & Cellular Proteomics. MCP 10, no. 12:Article No. M110.007302. PNNL-SA-77028. doi:10.1074/mcp.M110.007302