Staff information

Biography

Tao Liu is a senior scientist in the Integrative Omics Group in the Biological Sciences Division at PNNL. His work at PNNL has centered on developing and applying innovative methods and technologies including targeted proteomics (e.g., selected reaction monitoring) that enable high-throughput, sensitive, and quantitative LC-MS-based proteomics measurements of complex biological and clinical samples. Applications of these technologies include in-depth and robust characterization of tissue and biofluids such as blood plasma, breast proximal fluids, and cerebrospinal fluid to discover and verify disease-specific protein biomarkers. He is currently the principle investigator of the National Cancer Institute (NCI) Early Detection Research Network (EDRN) Biomarker Reference and Resource Center at PNNL, and project manager of several large-scale cancer studies including the NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) Proteome Characterization Center at PNNL. Many of these cancer projects integrate global proteomics data with protein post-translational modifications (PTMs; e.g., phosphorylation, O-GlcNAcylation) measurements and other omics data (e.g., genomics, glycomics).

Prior to joining PNNL, Dr. Liu was a postdoc at the Howard Hughes Medical Institute at the University of Washington. He received his B.S. degree in Chemistry from Nanchang University, China, in 1996 and a Ph.D. degree in Biochemistry and Molecular Biology in 2001 from Shanghai Institute of Biochemistry, Chinese Academy of Sciences.

Tao Liu, Integrative Omics

My Bibliography (NCBI)

Research Interests

• Quantitative proteomics and PTMs
• Biomarker discovery and verification
• Integrative omics and cancer biology
• Neurologic diseases (e.g., chronic fatigue, multiple sclerosis)

Education and Credentials

• Ph.D., Biochemistry and Molecular Biology, Shanghai Institute of Biochemistry, Chinese Academy of Sciences, Shanghai, China, 2001
• B.S., Chemistry, Nanchang University, Nanchang, China, 1996

Affiliations and Professional Service

• Member, American Society for Mass Spectrometry
• Editorial Board of Frontiers in MicroBiotechnology
• Ad-hoc grant reviewer for Emerging Technologies and Training Neurosciences, NIH

Awards and Recognitions

• 1999 Ying-Lai Wang Award, Shanghai Institute of Biochemistry
• 1996 Hong-Bing Wang Award, Nanchang University
• 1994 Xiang-Mei Chen Award, Nanchang University
• 1992-1996 The First Class Scholarship (each year), Nanchang University

PNNL Publications

2017

• Park JK, PD Piehowski, CS Wilkins, M Zhou, JA Mendoza, GM Fujimoto, BC Gibbons, JB Shaw, Y Shen, AK Shukla, RJ Moore, T Liu, VA Petyuk, N Tolic, L Pasa Tolic, RD Smith, SH Payne, and S Kim. 2017. "Informed-Proteomics: Open Source Software Package for Top-down Proteomics." Nature Methods 14(9):909-914.  doi:10.1038/nmeth.4388
• 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 S, F Yang, VA Petyuk, AK Shukla, ME Monroe, MA Gritsenko, KD Rodland, RD Smith, W Qian, CX Gong, and T Liu. 2017. "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease." The Journal of Pathology 243(1):78-88.  doi:10.1002/path.4929

2016

• Gritsenko MA, Z Xu, T Liu, and RD Smith. 2016. "Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS." In Quantitative Proteomics by Mass Spectrometry, 2nd edition. Series: Methods in Molecular Biology, vol. 1410, ed. S Sechi, pp. 237-247.  Springer, New York, NY. 
• Shi T, E Song, S Nie, KD Rodland, T Liu, WJ Qian, and RD Smith. 2016. "Advances in targeted proteomics and applications to biomedical research." Proteomics 16(15-16):2160-2182.  doi:10.1002/pmic.201500449
• Burnum-Johnson KE, S Nie, CP Casey, ME Monroe, DJ Orton, YM Ibrahim, MA Gritsenko, TRW Clauss, AK Shukla, RJ Moore, SO Purvine, T Shi, W Qian, T Liu, ES Baker, and RD Smith. 2016. "Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Molecular and Cellular Proteomics 15(12):3694-3705.  doi:10.1074/mcp.M116.061143
• Hatakeyama H, SY Wu, YA Lyons, S Pradeep, W Wang, Q Huang, KA Court, T Liu, S Nie, C Rodriguez-Aguayo, F Shen, Y Huang, T Hisamatsu, T Mitamura, N Jennings, J Shim, PL Dornialk, LS Mangala, M Petrillo, VA Petyuk, AA Schepmoes, AK Shukla, M Torres-Lugo, JS Lee, KD Rodland, A Fagotti, G Lopez-Bernstein, C Li, and AK Sood. 2016. "Role of CTGF in Sensitivity to Hyperthermia in Ovarian and Uterine Cancers." Cell Reports 17(6):1621-1631.  doi:10.1016/j.celrep.2016.10.020
• Hoofnagle AN, JR Whiteaker, SA Carr, E Kuhn, T Liu, SA Massoni, SN Thomas, R Townsend, LJ Zimmerman, E Boja, J Chen, DL Crimmins, S Davies, Y Gao, TR Hiltke, K Ketchum, C Kinsinger, M Mesri, MR Meyer, W Qian, RM Schoenherr, M Scott, T Shi, G Whiteley, J Wrobel, C Wu, BL Ackermann, R Aebersold, DR Barnidge, DM Bunk, N Clarke, JB Fishman, RP Grant, U Kusebauch, MM Kushnir, MS Lowenthal, R Moritz , H Neubert, SD Patterson, AL Rockwood, J Rogers, RJ Singh, J Van Eyk , SH Wong, S Zhang, DW Chan, X Chen, MJ Ellis, D Liebler, KD Rodland, H Rodriguez, RD Smith, Z Zhang, H Zhang, and AG Paulovich. 2016. "Recommendations for the generation, quantification, storage and handling of peptides used for mass spectrometry-based assays." Clinical Chemistry 62(1):48-69.  doi:10.1373/clinchem.2015.250563
• Ruggles K, Z Tang, X Wang, H Grover, M Askenazi, J Teubl, S Cao, M McLennan, K Clauser, DL Tabb, P Mertins, R Slebos, P Erdmann-Gilmore, S Li, H Gunawardena, L Xie, T Liu, JY Zhou, S Sun, KA Hoadley, CM Perou, X Chen, S Davies, CA Maher, C Kinsinger, KD Rodland, H Zhang, Z Zhang, L Ding, R Townsend, H Rodriguez, DW Chan, RD Smith, D Liebler, SA Carr, SH Payne, M Ellis, and D Fenyo. 2016. "An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer." Molecular and Cellular Proteomics 15(3):1060-1071.  doi:10.1074/mcp.M115.056226
• Tabb DL, X Wang, SA Carr, K Clauser, P Mertins, MC Chambers, JD Holman, J Wang, B Zhang, LJ Zimmerman, X Chen, H Gunawardena, S Davies, M Ellis, S Li, R Townsend, E Boja, K Ketchum, C Kinsinger, M Mesri, H Rodriguez, T Liu, S Kim, JE McDermott, SH Payne, VA Petyuk, KD Rodland, RD Smith, F Yang, DW Chan, B Zhang, H Zhang, Z Zhang, JY Zhou, and D Liebler. 2016. "Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts." Journal of Proteome Research 15(3):691-706.  doi:10.1021/acs.jproteome.5b00859
• Wang H, T Shi, W Qian, T Liu, J Kagan, S Srivastava, RD Smith, KD Rodland, and DG Camp, II. 2016. "The Clinical Impact of Recent Advances in LC-MS for Cancer Biomarker Discovery and Verification." Expert Review of Proteomics 13(1):99-114.  doi:10.1586/14789450.2016.1122529
• Whiteaker JR, G Halusa, AN Hoofnagle, V Sharma, B MacLean, P Yan, J Wrobel, J Kennedy, DR Mani, LJ Zimmerman, MR Meyer, M Mesri, E Boja, SA Carr, DW Chan, X Chen, J Chen, S Davies, M Ellis, D Fenyo, T Hiltket, K Ketchum, C Kinsinger, E Kuhn, D Liebler, T Liu, M Loss, M MacCoss, W Qian, R Rivers, KD Rodland, K Ruggles, M Scott, RD Smith, SN Thomas, R Townsend, G Whiteley, C Wu, H Zhang, Z Zhang, H Rodriguez, and AG Paulovich. 2016. "Using the CPTAC Assay Portal to identify and implement highly characterized targeted proteomics assays ." In Quantitative Proteomics by Mass Spectrometry, 2nd edition. Series: Methods in Molecular Biology, vol. 1410, ed. S Sechi, pp. 223-263.  Springer, New York, NY.  doi:10.1007/978-1-4939-3524-6_13
• Wu C, J Duan, T Liu, RD Smith, and W Qian. 2016. "Contributions of Immunoaffinity Chromatography to Deep Proteome Profiling of Human Biofluids." Journal of Chromatography B 1021:57-68.  doi:10.1016/j.jchromb.2016.01.015
• Zhang H, T Liu, Z Zhang, SH Payne, B Zhang, JE McDermott, JY Zhou, VA Petyuk, L Chen, D Ray, S Sun, F Yang, L Chen, J Wang, P Shah, SW Cha, P Aiyetan, S Woo, Y Tian, MA Gritsenko, TRW Clauss, C Choi, ME Monroe, SN Thomas, S Nie, C Wu, RJ Moore, KH Yu, DL Tabb, D Fenyo, V Bafna, Y Wang, H Rodriguez, E Boja, T Hiltket, R Rivers, LJ Sokoll, H Zhu, IM Shih, L Cope, A Pandey, B Zhang, M Snyder, D Levine, RD Smith, DW Chan, and KD Rodland. 2016. "Integrated proteogenomic characterization of human high grade serous ovarian cancer." Cell 166(3):755-765.  doi:10.1016/j.cell.2016.05.069

2015

• 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
• Wang H, Y Yang, Y Li, B Bai, X Wang, H Tan, T Liu, TG Beach, J Peng, and Z Wu. 2015. "Systematic Optimization of Long Gradient Chromatography Mass Spectrometry for Deep Analysis of Brain Proteome." Journal of Proteome Research 14(2):829-838.  doi:10.1021/pr500882h
• Wu C, ME Monroe, Z Xu, GW Slysz, SH Payne, KD Rodland, T Liu, and RD Smith. 2015. "An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics." Journal of the American Society for Mass Spectrometry 26(12):2002-2008.  doi:10.1007/s13361-015-1169-z
• Wu C, T Liu, ES Baker, KD Rodland, and RD Smith. 2015. "Mass spectrometry for biomarker development." In General Methods in Biomarker Research and their Applications. Biomarkers in Disease: Methods, Discoveries and Applications, ed. V Preedy and V Patel, pp. 17-48.  Springer, Heidelberg , Germany. 
• 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

• Carr SA, SE Abbateillo, BL Ackermann, CH Borchers, B Domon, EW Deutsch, R Grant, AN Hoofnagle, R Huttenhain, JM Koomen, D Liebler, T Liu, B MacLean, DR Mani, E Mansfield, H Neubert, AG Paulovich, L Reiter, O Vitek, R Aebersold, LN Anderson, R Bethem, J Blonder, E Boja, J Botelho, M Boyne, RA Bradshaw, AS Burlingame, DW Chan, H Keshishian, E Kuhn, CR Kingsinger, JS Lee, SW Lee, RL Moritz, J Oses-Prieto, N Rifai, JE Ritchie, H Rodriguez, PR Srinivas, R Townsend, J Van Eyk , G Whiteley, A Wiita, and S Weintraub. 2014. "Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach." Molecular and Cellular Proteomics 13(3):907-917.  doi:10.1074/mcp.M113.036095
• Guo J, MJ Gaffrey, D Su, T Liu, DG Camp, II, RD Smith, and W Qian. 2014. "Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications." Nature Protocols 9(1):64-75.  doi:10.1038/nprot.2013.161
• 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
• Mertins P, F Yang, T Liu, DR Mani, VA Petyuk, M Gillette, K Clauser, J Qiao, MA Gritsenko, RJ Moore, D Levine, R Townsend, P Erdmann-Gilmore, JE Snider, S Davies, K Ruggles, D Fenyo, RT Kitchens, S Li, N Olvera, F Dao, H Rodriguez, DW Chan, D Liebler, F White, KD Rodland, G Mills, RD Smith, AG Paulovich, M Ellis, and SA Carr. 2014. "Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels." Molecular & Cellular Proteomics. MCP 13(7):1690-1704.  doi:10.1074/mcp.M113.036392
• 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
• Wang S, F Yang, DG Camp, II, KD Rodland, W Qian, T Liu, and RD Smith. 2014. "Proteomic Approaches for Site-specific O-GlcNAcylation Analysis." Bioanalysis 6(19):2571-2580.  doi:10.4155/bio.14.239
• Whiteaker JR, G Halusa, AN Hoofnagle, V Sharma, B MacLean, P Yan, J Wrobel, J Kennedy, DR Mani, LJ Zimmerman, MR Meyer, M Mesri, H Rodriguez, SE Abbateillo, E Boja, SA Carr, DW Chan, X Chen, J Chen, S Davies, M Ellis, D Fenyo, T Hiltket, K Ketchum, C Kinsinger, E Kuhn, D Liebler, D Lin, T Liu, M Loss, M MacCoss, W Qian, R Rivers, KD Rodland, K Ruggles, M Scott, RD Smith, SN Thomas, R Townsend, G Whiteley, C Wu, H Zhang, Z Zhang, and AG Paulovich. 2014. "CPTAC Assay Portal: a repository of targeted proteomic assays." Nature Methods 11(7):703-704.  doi:10.1038/nmeth.3002
• Woo S, SW Cha, S Na, C Guest, T Liu, RD Smith, KD Rodland, SH Payne, and V Bafna. 2014. "Proteogenomic strategies for identification of aberrant cancer peptides using large-scale Next Generation Sequencing data." Proteomics 14(23-24):2719-2730.  doi:10.1002/pmic.201400206
• 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

• Finnerty CC, MG Jeschke, W Qian, A Kaushal, W Xiao, T Liu, MA Gritsenko, RJ Moore, DG Camp, II, LL Moldawer, C Elson, D Schoenfeld, R Gamelli, N Gibran, M Klein, B Arnoldo, D Remick, RD Smith, RW Davis, RG Tompkins, and DN Herndon. 2013. "DETERMINATION OF BURN PATIENT OUTCOME BY LARGE-SCALE QUANTITATIVE DISCOVERY PROTEOMICS." Critical Care Medicine 41(6):1421-1434.  doi:10.1097/CCM.0b013e31827c072e
• Schutzer SE, TE Angel, T Liu, AA Schepmoes, F Xie, JP Bergquist, L Vecsei, D Zadori, DG Camp, II, BK Holland, RD Smith, and PK Coyle. 2013. "Gray Matter Is Targeted in First-Attack Multiple Sclerosis." PLoS One 8(9):E6617.  doi:10.1371/journal.pone.0066117
• 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

2012

• Baker ES, T Liu, VA Petyuk, KE Burnum-Johnson, YM Ibrahim, GA Anderson, and RD Smith. 2012. "Mass Spectrometry for Translational Proteomics: Progress and Clinical Implications." Genome Medicine 4:Article No. 63.  doi:10.1186/gm364
• Hu Z, ER Browne, T Liu, TE Angel, PC Ho, and E Chun Yong Chan. 2012. "Metabonomic Profiling of TASTPM Transgenic Alzheimer's Disease Mouse Model ." Journal of Proteome Research 11(12):5903-5913.  doi:10.1021/pr300666p
• Chauvin T, F Xie, T Liu, CD Nicora, F Yang, DG Camp, II, RD Smith, and KP Roberts. 2012. "A Systematic Analysis of a Deep Mouse Epididymal Sperm Proteome." Biology of Reproduction 87(6):Article No. 141.  doi:10.1095/biolreprod.112.104208
• 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, D Su, T Liu, K Tang, DG Camp, II, W Qian, and RD Smith. 2012. "Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics." Proteomics 12(8):1074-1092.  doi:10.1002/pmic.201100436
• 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
• Wang L, UK Aryal, Z Dai, AC Mason, ME Monroe, Z Tian, J Zhou, D Su, KK Weitz, T Liu, DG Camp, II, RD Smith, SE Baker, and W Qian. 2012. "Mapping N-linked Glycosylation Sites in the Secretome and Whole Cells of Aspergillus niger Using Hydrazide Chemistry and Mass Spectrometry." Journal of Proteome Research 11(1):143-56.  doi:10.1021/pr200916k
• Waters KM, T Liu, RD Quesenberry, AR Willse, S Bandyopadhyay, LE Kathmann, TJ Weber, RD Smith, HS Wiley, and BD Thrall. 2012. "Network Analysis of Epidermal Growth Factor Signaling using Integrated Genomic, Proteomic and Phosphorylation Data ." PLoS One 7(3):Article No. e34515.  doi:10.1371/journal.pone.0034515
• Zhou J, GP Dann, T Shi, L Wang, X Gao, D Su, CD Nicora, AK Shukla, RJ Moore, T Liu, DG Camp, II, RD Smith, and W Qian. 2012. "Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications." Analytical Chemistry 84(6):2862-2867.  doi:10.1021/ac203394r

2011

• Hossain M, DT Kaleta, EW Robinson, T Liu, R Zhao, JS Page, RT Kelly, RJ Moore, K Tang, DG Camp, II, W Qian, and RD Smith. 2011. "Enhanced Sensitivity for Selected Reaction Monitoring-Mass Spectrometry-based Targeted Proteomics using a Dual-Stage Electrodynamic Ion Funnel Interface ." Molecular & Cellular Proteomics. MCP 10(2):, doi:10.1074/mcp.M000062-MCP201
• 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
• Schoenherr RM, KS Kelly-Spratt, CW Lin, JR Whiteaker, T Liu, T Holzman, I Coleman, LC Feng, TD Lorentzen, AL Krasnoselsky, P Wang, Y Liu, KE Gurley, LM Amon, AA Schepmoes, RJ Moore, DG Camp, II, LA Chodosh, RD Smith, PS Nelson, M McIntosh, C Kemp, and AG Paulovich. 2011. "Proteome and Transcriptome Profiles of a Her2/Neu-driven Mouse Model of Breast Cancer." Proteomics - Clinical Applications 5(3-4):179-188.  doi:10.1002/prca.201000037
• Schutzer SE, TE Angel, T Liu, AA Schepmoes, TRW Clauss, JN Adkins, DG Camp, II, BK Holland, J Bergquist, PK Coyle, RD Smith, BA Fallon, and B Natelson. 2011. "Distinct Cerebrospinal Fluid Proteomes Differentiate Post-Treatment Lyme Disease from Chronic Fatigue Syndrome." PLoS One 6(2):Article No. e17287.  doi:10.1371/journal.pone.0017287
• Wang Y, F Yang, MA Gritsenko, Y Wang, TRW Clauss, T Liu, Y Shen, ME Monroe, D Lopez-Ferrer, T Reno, RJ Moore, RL Klemke, DG Camp, II, and RD Smith. 2011. "Reversed-Phase Chromatography with Multiple Fraction Concatenation Strategy for Proteome Profiling of Human MCF10A Cells." Proteomics 11(10):2019-2026.  doi:10.1002/pmic.201000722
• Xie F, T Liu, W Qian, VA Petyuk, and RD Smith. 2011. "Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics." Journal of Biological Chemistry 286(29):25443-25449. 
• Zhang H, KE Burnum, ML Luna, BO Petritis, JS Kim, W Qian, RJ Moore, A Heredia-Langner, BJM Webb-Robertson, BD Thrall, DG Camp, II, RD Smith, JG Pounds, and T Liu. 2011. "Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size." Proteomics 11(23):4569-4577.  doi:10.1002/pmic.201100037

2010

• Schutzer SE, T Liu, B Natelson, TE Angel, AA Schepmoes, SO Purvine, KK Hixson, MS Lipton, DG Camp, II, PK Coyle, RD Smith, and J Bergquist. 2010. "Establishing the Proteome of Normal Human Cerebrospinal Fluid ." PLoS One 5(6):e10980-.  doi:10.1371/journal.pone.0010980
• Shen Y, N Tolic, T Liu, R Zhao, BO Petritis, MA Gritsenko, DG Camp, II, RJ Moore, SO Purvine, FJ Esteva, and RD Smith. 2010. " Blood Peptidome-Degradome Profile of Breast Cancer." PLoS One 5(10):Article No.: e13133.  doi:10.1371/journal.pone.0013133
• Shen Y, T Liu, N Tolic, BO Petritis, R Zhao, RJ Moore, SO Purvine, DG Camp, II, and RD Smith. 2010. "A strategy for degradomic-peptidomic analysis of the human blood plasma ." Journal of Proteome Research 9(5):2339-2346.  doi:10.1021/pr901083m

2009

• Qian W, T Liu, VA Petyuk, MA Gritsenko, BO Petritis, AD Polpitiya, A Kaushal, W Xiao, CC Finnerty, MG Jescheke, N Jaitly, ME Monroe, RJ Moore, LL Moldawer, RW Davis, RG Tompkins, DN Hemdon, DG Camp, II, and RD Smith. 2009. "Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an O-18-Labeled “Universal” Reference Sample ." Journal of Proteome Research 8(1):290-299. 

2008

• Pertz OC, Y Wang, F Yang, W Wang, J gay, MA Gritsenko, TRW Clauss, DJ Anderson, T Liu, KJ Auberry, DG Camp, II, RD Smith, and RL Klemke. 2008. "“Spatial Mapping of the Neurite and Soma Proteomes Reveals a Functional Cdc42/Rac Regulatory Network”." Proceedings of the National Academy of Sciences of the United States of America 105(6):1931-1936.  doi:10.1073/pnas.0706545105
• Qian W, DT Kaleta, BA Ogata, H Jiang, T Liu, X Zhang, HM Mottaz, SM Varnum, DG Camp, II, huang, X Fang, W Zhang, and RD Smith. 2008. "Enhanced Detection of Low Abundant Human Plasma Proteins using a Tandem IgY12-SuperMix Immunoaffinity Separation Strategy." Molecular & Cellular Proteomics. MCP 7(10):1963-1973.  doi:10.1074/mcp.M800008-MCP200
• Rogers S, M Girolami, W Kolch, KM Waters, T Liu, BD Thrall, and HS Wiley. 2008. "Investigating the Correspondence Between Transcriptomic and Proteomic Expression Profiles Using Coupled Cluster Models." Bioinformatics 24(24):2894-2900.  doi:10.1093/bioinformatics/btn553

2007

• Chan EY, W Qian, DL Diamond, T Liu, MA Gritsenko, ME Monroe, DG Camp, II, RD Smith, and MG Katze. 2007. "Quantitative analysis of human immunodeficiency virus type 1-infected CD4(+) cell proteome: Dysregulated cell cycle progression and nuclear transport coincide with robust virus production." Journal of Virology 81(14):7571-7583. 
• Liu T, W Qian, DG Camp, II, and RD Smith. 2007. "The Use of a Quantitative Cysteinyl-peptide Enrichment Technology for High-Throughput Quantitative Proteomics." In Quantitative Proteomics by Mass Spectrometry, Methods in Molecular Biology, vol. 359, pp. 107-24.  Humana Press, Totowa, NJ. 
• Liu T, ME Belov, N Jaitly, W Qian, and RD Smith. 2007. "Accurate Mass Measurements in Proteomics." Chemical Reviews 107(8):3621-3653.  doi:10.1021/cr068288j
• Whiteaker JR, H Zhang, JK Eng, R Fang, BD Piening, LC Feng, TD lorentzen, RM Schoenherr, JF Keane, T Holzman, M Fitzgibbon, CW Lin, H Zhang, K Cooke, T Liu, DG Camp, II, LN Anderson, J Watts, RD Smith, M McIntosh, and AG Paulovich. 2007. "Head-to-Head Comparison of Serum Fractionation Techniques." Journal of Proteome Research 6(2):828-836.  doi:10.1021/pr0604920

2006

• Qian W, JM Jacobs, T Liu, DG Camp, II, and RD Smith. 2006. "Advances and Challenges in Liquid Chromatography-Mass Spectrometry-Based Proteomics Profiling for Clinical Applications." Molecular & Cellular Proteomics. MCP 5(10):1727-1744.  doi:10.1074/mcp.M600162-MCP200
• Liu T, W Qian, HM Mottaz, MA Gritsenko, AD Norbeck, RJ Moore, SO Purvine, DG Camp, II, and RD Smith. 2006. "Evaluation of Multi-Protein Immunoaffinity Subtraction for Plasma Proteomics and Candidate Biomarker Discovery Using Mass Spectrometry ." Molecular & Cellular Proteomics. MCP 5(11):2167-2174. 
• Liu T, W Qian, MA Gritsenko, W Xiao, LL Moldawer, A Kaushal, ME Monroe, SM Varnum, RJ Moore, SO Purvine, RV Maier, RW Davis, RG Tompkins, DG Camp, II, and RD Smith. 2006. "High Dynamic Range Characterization of the Trauma Patient Plasma Proteome ." Molecular & Cellular Proteomics. MCP 5(10):1899-1913.  doi:10.1074/mcp.M600068-MCP200
• Wang HH, W Qian, MH Chin, VA Petyuk, RC Barry, T Liu, MA Gritsenko, HM Mottaz, RJ Moore, DG Camp, II, AH Khan, D Smith, and RD Smith. 2006. "Characterization of the Mouse Brain Proteome Using Global Proteomic Analysis Complemented with Cysteinyl-Peptide Enrichment." Journal of Proteome Research 5(2):361-369. 

2005

• Qian W, ME Monroe, T Liu, JM Jacobs, GA Anderson, Y Shen, RJ Moore, DJ Anderson, R Zhang, SE Calvano, SF Lowry, W Xiao, LL Moldawer, RW Davis, RG Tompkins, DG Camp, II, and RD Smith. 2005. "Quantitative Proteome Analysis of Human Plasma Following in vivo Lipopolysaccharide Administration using O-16/O-18 Labeling and the Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 4(5):700-709. 
• Qian W, T Liu, ME Monroe, EF Strittmatter, JM Jacobs, LJ Kangas, K Petritis, DG Camp, II, and RD Smith. 2005. "Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis: The Human Proteome." Journal of Proteome Research 4(1):53-62. 
• Jacobs JM, JN Adkins, W Qian, T Liu, Y Shen, DG Camp, II, and RD Smith. 2005. "Utilizing human blood plasma for proteomic biomarker discovery." Journal of Proteome Research 4(4):1073-1085.  doi:10.1021/pr0500657
• Liu T, W Qian, MA Gritsenko, DG Camp, II, ME Monroe, RJ Moore, and RD Smith. 2005. "Human Plasma N-Glycoproteome Analysis by Immunoaffinity Subtraction, Hydrazide Chemistry, and Mass Spectrometry." Journal of Proteome Research 4(6):2070-2080. 
• Liu T, W Qian, WNU Chen, JM Jacobs, RJ Moore, DJ Anderson, MA Gritsenko, ME Monroe, BD Thrall, DG Camp, II, and RD Smith. 2005. "Improved Proteome Coverage by Using High Efficiency Cysteinyl-peptide Enrichment: The Human Mammary Epithelial Cell Proteome." Proteomics 5(5):1263-1273. 

2004

• Liu T, W Qian, EF Strittmatter, DG Camp, II, GA Anderson, BD Thrall, and RD Smith. 2004. "High throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology." Analytical Chemistry 76(18):5345-5353.