Tujin Shi is a senior scientist in the Integrative Omics group of the Biological Sciences Division at PNNL, where he has worked since 2010. His research centers on the development and applications of mass spectrometry-based approaches to address current biological and biomedical need. He has broad research experiences from fundamental research to biological sciences. His current research involves the development of ultrasensitive targeted proteomics and convenient single-cell proteomics technologies and their applications for absolute quantification of signaling pathway dynamics, preclinical verification of disease biomarkers, spatial proteome mapping of mammalian tissues, and protein analysis of small subpopulations of tumor cells from liquid (tissue) biopsy. Shi is currently a senior member of multiple National Institutes of Health (NIH) research programs and principal investigator of two NIH-funded projects. He is author or co-author of more than 80 articles in peer-reviewed scientific journals and has served as a reviewer for more than 20 scientific journals. In addition to research, Shi is actively involved in training and mentoring postdoctoral researchers, junior staff, and interns.

Disciplines and Skills

  • Targeted proteomics
  • Single-cell proteomics
  • Liquid (tissue) biopsy proteomics
  • Disease biomarker and biology
  • Signal transduction
  • Gas-phase ion chemistry


  • PhD in Bioanalytical Chemistry, York University
  • PhD in Physical Chemistry, Institute of Chemistry
  • MS in Physical Chemistry, Beijing Normal University
  • BS in Chemistry, Jiangxi Normal University

Affiliations and Professional Service

  • American Chemistry Society
  • American Society for Mass Spectrometry



  • 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
  • Gerosa L., C. Chidley, F. Frohlich, G. Sanchez, S.K. Lim, J. Muhlich, and J. Chen, et al. 2020. "Receptor-driven ERK pulses reconfigure MAPK signaling and enable persistence of drug-adapted BRAF-mutant melanoma cells." Cell Systems 11, no. 5:478-494.e9. PNNL-SA-156751. doi:10.1016/j.cels.2020.10.002
  • Habowski A.N., J.L. Flesher, J.M. Bates, C. Tsai, K.D. Martin, R. Zhao, and A.K. Ganesan, et al. 2020. "Transcriptomic and Proteomic Signatures of Stemness and Differentiation in the Colon Crypt." Communications Biology 3. PNNL-SA-153928. doi:10.1038/s42003-020-01181-z
  • Kagan J., R.L. Moritz, R. Mazurchuk, J. Lee, P. Kharchenko, O. Rozenblatt-Rosen, and E. Ruppin, et al. 2020. "National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions." Journal of Proteome Research 19, no. 5:1900-1912. PNNL-SA-152101. doi:10.1021/acs.jproteome.0c00021
  • 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
  • Li M., R. Li, Y. Gao, C.T. Resch, W. Qian, T. Shi, and L. Shi, et al. 2020. "Nitrate bioreduction dynamics in hyporheic zone sediments under cyclic changes of chemical compositions." Journal of Hydrology 585. PNNL-SA-152190. doi:10.1016/j.jhydrol.2020.124836
  • Martin K.D., T. Zhang, P. Zhang, W.B. Chrisler, T.L. Fillmore, F. Liu, and T. Liu, et al. 2020. "Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells." Journal of Visualized Experiments (JoVE). PNNL-SA-153959. doi:10.3791/61797
  • Tsai C., R. Zhao, S.M. Williams, R.J. Moore, K.D. Schultz, W.B. Chrisler, and L. Pasa Tolic, et al. 2020. "An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics." Molecular and Cellular Proteomics 19, no. 5:828-838. PNNL-SA-149183. doi:10.1074/mcp.RA119.001857
  • Wang Y., T. Shi, S. Srivastava, J. Kagan, T. Liu, and K.D. Rodland. 2020. "Proteomic Analysis of Exosomes for Discovery of Protein Biomarkers for Prostate and Bladder Cancer." Cancers 12, no. 9:2335. PNNL-SA-154352. doi:10.3390/cancers12092335


  • 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
  • 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
  • Tsai C., J.S. Smith, K. Krajewski, R. Zhao, A.M. Moghieb, C.D. Nicora, and X. Xiong, et al. 2019. "Tandem Mass Tag Labeling Facilitates Reversed-Phase Liquid Chromatography-Mass Spectrometry Analysis of Hydrophilic Phosphopeptides." Analytical Chemistry 91, no. 18:11606-11613. PNNL-SA-142808. doi:10.1021/acs.analchem.9b01814
  • Wu H., L. Yi, R. Wojcik, T. Shi, and K. Tang. 2019. "A Separation Voltage Polarity Switching Method for Higher Sample Loading Capacity and Better Separation Resolution in Transient Capillary Isotachophoresis Separation." Analyst 144, no. 2:454-462. PNNL-SA-135251. doi:10.1039/C8AN01779D
  • Yi L., C. Tsai, E. Dirice, A.C. Swensen, J. Chen, T. Shi, and M.A. Gritsenko, et al. 2019. "Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells." Analytical Chemistry 91, no. 9:5794-5801. PNNL-SA-140381. doi:10.1021/acs.analchem.9b00024
  • 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


  • Chouinard C.D., G. Nagy, I.K. Webb, T. Shi, E.M. Baker, S.A. Prost, and T. Liu, et al. 2018. "Improved Sensitivity and Separations for Phosphopeptides using Online Liquid Chromotography Coupled with Structures for Lossless Ion Manipulations Ion Mobility-Mass Spectrometry." Analytical Chemistry 90, no. 18:10889-10896. PNNL-SA-135107. doi:10.1021/acs.analchem.8b02397
  • Orwoll E.S., J. Wiedrick, J.M. Jacobs, E.M. Baker, P.D. Piehowski, V.A. Petyuk, and Y. Gao, et al. 2018. "High-throughput serum proteomics for the identification of protein biomarkers of mortality in older men." Aging Cell 17, no. 2:Article No. e12717. PNNL-SA-131443. doi:10.1111/acel.12717
  • 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 Chemistry90, 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


  • 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
  • Wang H., C.E. Barbieri, J. He, Y. Gao, T. Shi, C. Wu, and A.A. Schepmoes, et al. 2017. "Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics." Journal of Translational Medicine 15. PNNL-SA-125993. doi:10.1186/s12967-017-1276-7


  • Burnum-Johnson K.E., S. Nie, C.P. Casey, M.E. Monroe, D.J. Orton, Y.M. Ibrahim, and M.A. Gritsenko, et al. 2016. "Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Molecular and Cellular Proteomics 15, no. 12:3694-3705. PNNL-SA-118308. doi:10.1074/mcp.M116.061143
  • Hoofnagle A.N., J.R. Whiteaker, S.A. Carr, E. Kuhn, T. Liu, S.A. Massoni, and S.N. Thomas, et al. 2016. "Recommendations for the generation, quantification, storage and handling of peptides used for mass spectrometry-based assays." Clinical Chemistry 62, no. 1:48-69. PNNL-SA-113208. doi:10.1373/clinchem.2015.250563
  • Nielson C., K. Jones, R.F. Chun, J.M. Jacobs, Y. Wang, M. Hewison, and J.S. Adams, et al. 2016. "Free 25-Hydroxyvitamin D: Impact of Vitamin D Binding Protein Assays on Racial-Genotypic Associations." Journal of Clinical Endocrinology and Metabolism 101, no. 5:2226-2234. PNNL-SA-120076. doi:10.1210/jc.2016-1104
  • Nielson C., K. Jones, R.F. Chun, J.M. Jacobs, Y. Wang, M. Hewison, and J.S. Adams, et al. 2016. "Role of Assay Type in Determining Free 25-Hydroxyvitamin D Levels in Diverse Populations." The New England Journal of Medicine 374, no. 17:1695-1696. PNNL-SA-108708. doi:10.1056/NEJMc1513502
  • Shi T., E. Song, S. Nie, K.D. Rodland, T. Liu, W. Qian, and R.D. Smith. 2016. "Advances in targeted proteomics and applications to biomedical research." Proteomics 16, no. 15-16:2160-2182. PNNL-SA-120776. doi:10.1002/pmic.201500449
  • Shi T., M. Niepel, J.E. McDermott, Y. Gao, C.D. Nicora, W.B. Chrisler, and L.M. Markillie, et al. 2016. "Conservation of Protein Abundance Patterns Reveals the Regulatory Architecture of the of the EGFR-MAPK Pathway." Science Signaling 9, no. 436:rs6. PNNL-SA-115056. doi:10.1126/scisignal.aaf0891
  • 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
  • Wang H., T. Shi, W. Qian, T. Liu, J. Kagan, S. Srivastava, and R.D. Smith, et al. 2016. "The Clinical Impact of Recent Advances in LC-MS for Cancer Biomarker Discovery and Verification." Expert Review of Proteomics13, no. 1:99-114. PNNL-SA-113659. doi:10.1586/14789450.2016.1122529


  • 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


  • 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
  • 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


  • Shi T., and W. Qian. 2013. "Antibody-free PRISM-SRM for multiplexed protein quantification: Is this the new competition for immunoassays in bioanalysis?." Bioanalysis 5, no. 3:267-269. PNNL-SA-92465. doi:10.4155/bio.12.336
  • 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
  • Zhou J., R.K. Krovvidi, Y. Gao, H. Gao, B.O. Petritis, A. De, and C. Miller-Graziano, et al. 2013. "Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling." Proteomics - Clinical Applications 7, no. 7-8:571-583. PNWD-SA-9434. doi:10.1002/prca.201200109


  • 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., D. Su, T. Liu, K. Tang, D.G. Camp, W. Qian, and R.D. Smith. 2012. "Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics." Proteomics 12, no. 8:1074-1092. PNNL-SA-82133. doi:10.1002/pmic.201100436
  • Shi T., J. Zhou, M.A. Gritsenko, M. Hossain, D.G. Camp, R.D. Smith, and W. Qian. 2012. "IgY14 and SuperMix immunoaffinity separations coupled with liquid chromatography-mass spectrometry for human plasma proteomic biomarker discovery." Methods 56, no. 2:246-253. PNNL-SA-80317. doi:10.1016/j.ymeth.2011.09.001
  • 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 America109, no. 38:15395-15400. PNNL-SA-83776. doi:10.1073/pnas.1204366109
  • Zhou J., G.P. Dann, T. Shi, L. Wang, X. Gao, D. Su, and C.D. Nicora, et al. 2012. "Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications." Analytical Chemistry 84, no. 6:2862-2867. PNNL-SA-84751. doi:10.1021/ac203394r