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

2025

• Kitata R., M. Velickovic, Z. Xu, R. Zhao, D. Scholten, R.K. Chu, and D.J. Orton, et al. 2025. "Robust collection and processing for label-free single voxel proteomics." Nature Communications 16:Art No. 547. PNNL-SA-190368. doi:10.1038/s41467-024-54643-x

2024

• Abhange K., R. Kitata, J. Zhang, Y. Wang, M.J. Gaffrey, T. Liu, and V. Gunchick, et al. 2024. "In-depth proteome profiling of small extracellular vesicles isolated from cancer cell lines and patient serum." Journal of Proteome Research 23, no. 1:386-396. PNNL-SA-190106. doi:10.1021/acs.jproteome.3c00614
• Chen H., Y. Fu, M. Han, X. Han, L. Hao, T. Huan, and L. Huang, et al. 2024. "Meeting Report on the 3rd Chinese American Society for Mass Spectrometry Conference - Advancing Biological and Pharmaceutical Mass Spectrometry." Biomedical Chromatography 38, no. 3:Art. No. e5795. PNNL-SA-191876. doi:10.1002/bmc.5795
• Diaz Ludovico I., S.M. Powell, G.M. Many, L.M. Bramer, S. Sarkar, K.G. Stratton, and T. Liu, et al. 2024. "A fast and sensitive size-exclusion chromatography method for plasma extracellular vesicle proteomic analysis." Proteomics 24, no. 16:2400025. PNNL-SA-194254. doi:10.1002/pmic.202400025
• Gao Y., H. Kim, R. Kitata, T. Lin, A.C. Swensen, T. Shi, and T. Liu. 2024. "Multiplexed Quantitative Proteomics in Prostate Cancer Biomarker Development." In Current Status of Prostate Cancer: Diagnosis, Biomarkers and Therapies, edited by Semmes, O. John, Nyalwidhe, J.O., Swadesh, K. Das, Fisher, Paul, B. 31-70. PNNL-SA-194316.
• Gluth A., X. Li, M.A. Gritsenko, M.J. Gaffrey, D. Kim, P.M. Lalli, and R.K. Chu, et al. 2024. "Integrative Multi-PTM Proteomics Reveals Dynamic Global, Redox, Phosphorylation, and Acetylation Regulation in Cytokine-treated Pancreatic Beta Cells." Molecular & Cellular Proteomics 23, no. 12:100881. PNNL-SA-202916. doi:10.1016/j.mcpro.2024.100881
• Gritsenko M.A., C. Tsai, H. Kim, and T. Liu. 2024. "Automated Immunoprecipitation Workflow for Comprehensive Acetylome Analysis." In Proteomics for Drug Discovery. Methods in Molecular Biology, edited by J. Blonder. 173-191. New York, New York:Humana Press. PNNL-SA-191447. doi:10.1007/978-1-0716-3922-1_12
• Harrison A.L., J.G. Eder, P.M. Lalli, N. Munoz Munoz, Y. Gao, C.S. Clendinen, and D.J. Orton, et al. 2024. "PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data." Journal of the American Society for Mass Spectrometry 35, no. 11:2680-2689. PNNL-SA-197329. doi:10.1021/jasms.4c00146
• Joshi S.K., P.D. Piehowski, T. Liu, S. Gosline, J.E. McDermott, B. Druker, and E. Traer, et al. 2024. "Mass spectrometry-based proteogenomics: New therapeutic opportunities for precision medicine." Annual Review of Pharmacology and Toxicology 64. PNNL-SA-182628. doi:10.1146/annurev-pharmtox-022723-113921
• Lin H., M. Mohammadhosseini, J. McClatchy, M. Villamor-Paya, S. Jeng, D. Bottomly, and C. Tsai, et al. 2024. "The TLK-ASF1 histone chaperone pathway plays a critical role in IL-1B-mediated AML progression." Blood 143, no. 26:2749-2762. PNNL-SA-185293. doi:10.1182/blood.2023022079
• Liu J., S. Cao, K.J. Imbach, M.A. Gritsenko, T.M. Lih, J.E. Kyle, and T.M. Yaron, et al. 2024. "Multi-scale signaling and tumor evolution in high-grade gliomas." Cancer Cell 42, no. 7:P1217-1238.E19. PNNL-SA-189873. doi:10.1016/j.ccell.2024.06.004
• Liu Z., M. Ng, S. Srivastava, T. Li, J. Liu, T. Phu, and B. Mateescu, et al. 2024. "Label-Free Single-Vesicle Based Surface Enhanced Raman Spectroscopy: A Robust Approach for Investigating the Biomolecular Composition of Small Extracellular Vesicles." PLoS One 19, no. 6:Art No. e0305418. PNNL-SA-176811. doi:10.1371/journal.pone.0305418
• Pino J.C., J.C. Posso Escobar, S.K. Joshi, M.D. Nestor, J. Moon, J.R. Hansen, and C.M. Hutchinson, et al. 2024. "Mapping the proteogenomic landscape enables prediction of drug response in acute myeloid leukemia." Cell Reports Medicine 5, no. 1:Art. No. 101359. PNNL-SA-185276. doi:10.1016/j.xcrm.2023.101359
• Tsai C., C. Hsu, Y. Wang, H. Kim, and T. Liu. 2024. "A Tip-based Workflow for Sensitive IMAC-based Low Nanogram Level Phosphoproteomics." In Proteomics for Drug Discovery. Methods in Molecular Biology, edited by J. Blonder. 129-140. New York, New York:Humana Press. PNNL-SA-191845. doi:10.1007/978-1-0716-3922-1_9

2023

• Dou Y., L. Katsnelson, M.A. Gritsenko, Y. Hu, B. Reva, R. Hong, and Y. Wang, et al. 2023. "Proteogenomic insights suggest druggable pathways in endometrial carcinoma." Cancer Cell 41, no. 9:1586-1605.e15. PNNL-SA-177735. doi:10.1016/j.ccell.2023.07.007
• Madda R., V.A. Petyuk, Y. Wang, T. Shi, C. Shriver, K.D. Rodland, and T. Liu. 2023. "Use of Longitudinal Serum Analysis and Machine Learning to Develop a Classifier for Cancer Early Detection." In Serum/Plasma Proteomics: Methods and Protocols. Methods in Moleculary Biology, edited by D.W. Greening and R.J. Simpson. 579-592. New York, New York:Humana. PNNL-ACT-SA-10675. doi:10.1007/978-1-0716-2978-9_33
• Tsai C., Y. Wang, C. Hsu, R. Kitata, R.K. Chu, M. Velickovic, and R. Zhao, et al. 2023. "A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics." Communications Biology 6, no. 1:Art. No. 70. PNNL-SA-171979. doi:10.1101/2022.04.12.488038
• Yao L., J. Wang, R.G. Jayasinghe, J. O'Neal, C. Tsai, M.P. Rettig, and Y. Song, et al. 2023. "Single-cell discovery and multiomic characterization of therapeutic targets in multiple myeloma." Cancer Research 83, no. 8:1214-1233. PNNL-SA-172699. doi:10.1158/0008-5472.CAN-22-1769
• You Y., C. Tsai, R. Patel, S. Sarkar, G. Clair, M. Zhou, and T. Liu, et al. 2023. "Analysis of a macrophage carbamylated proteome reveals a function in post-translational modification crosstalk." Cell Communication and Signaling 21, no. 1:241. PNNL-SA-186292. doi:10.1186/s12964-023-01257-3
• Zhong H., J. Zhu, S. Liu, D.H. Ghoneim, P. Surendran, T. Liu, and S. Fahle, et al. 2023. "Identification of blood protein biomarkers associated with prostate cancer risk using genetic prediction models: analysis of over 140,000 subjects." Human Molecular Genetics 32, no. 22:3181 - 3193. PNNL-SA-176816. doi:10.1093/hmg/ddad139

2022

• Kennedy J., J.R. Whiteaker, R.G. Ivey, A. Burian, S. Chowdhury, C. Tsai, and T. Liu, et al. 2022. "Internal standard triggered-parallel reaction monitoring mass spectrometry enables multiplexed quantification of candidate biomarkers in plasma." Analytical Chemistry 94, no. 27:9540 - 9547. PNNL-SA-166618. doi:10.1021/acs.analchem.1c04382
• Lin A., P.D. Piehowski, C. Tsai, T. Makushok, L. Yi, U. Diaz, and C. Yan, et al. 2022. "Determining protein polarization proteome-wide using physical dissection of individual Stentor coeruleus cells." Current Biology 32, no. 10:2300 - 2308.e4. PNNL-SA-172410. doi:10.1016/j.cub.2022.03.078
• Ramos E.K., C. Tsai, Y. Jia, Y. Cao, M. Manu, R. Taftaf, and A.D. Hoffman, et al. 2022. "Machine learning-assisted elucidation of CD81-CD44 interactions in promoting cancer stemness and extracellular vesicle integrity." eLife 11. PNNL-SA-177252. doi:10.7554/eLife.82669
• Sanford J.A., Y. Wang, J.R. Hansen, M.A. Gritsenko, K.K. Weitz, T.J. Sagendorf, and C.E. Tognon, et al. 2022. "Evaluation of differential peptide loading on tandem mass tag-based proteomic and phosphoproteomic data quality." Journal of the American Society for Mass Spectrometry 33, no. 1:17-30. PNNL-SA-155168. doi:10.1021/jasms.1c00169
• Wei X., L. Zhang, Y. Zhang, C. Cooper, C. Brewer, C. Tsai, and Y. Wang, et al. 2022. "Ablating Lgr5-expressing prostatic stromal cells activates the ERK-mediated mechanosensory signaling and disrupts prostate tissue homeostasis." Cell Reports 40, no. 10:Art. No. 111313. PNNL-SA-174213. doi:10.1016/j.celrep.2022.111313

2021

• Elmas A., S. Tharakan, S. Jaladanki, M.D. Galsky, T. Liu, and K. Huang. 2021. "Pan-cancer Proteogenomic Investigations Identify Post-Transcriptional Kinase Targets." Communications Biology 4, no. 1:Article No. 1112. PNNL-SA-154219. doi:10.1038/s42003-021-02636-7
• Jiang W., B. Wen, K. Li, W. Zeng, F. Leprevost, J. Moon, and V.A. Petyuk, et al. 2021. "Deep learning-derived evaluation metrics enable effective benchmarking of computational tools for phosphopeptide identification." Molecular & Cellular Proteomics. MCP 20. PNNL-SA-167275. doi:10.1016/j.mcpro.2021.100171
• Joshi S.K., T. Nechiporuk, D. Bottomly, P.D. Piehowski, J. Reisz, J. Pittsenbarger, and A. Kaempf, et al. 2021. "The AML microenvironment catalyzes a step-wise evolution to gilteritinib resistance." Cancer Cell 39, no. 7:999-1014. PNNL-SA-161620. doi:10.1016/j.ccell.2021.06.003
• Ma S., L.S. Mangala, W. Hu, E. Bayaktar, A. Yokoi, W. Hu, and S. Pradeep, et al. 2021. "CD63-mediated cloaking of VEGF in small extracellular vesicles contributes to anti-VEGF therapy resistance." Cell Reports 36, no. 7:Art. No. 109549. PNNL-SA-154216. doi:10.1016/j.celrep.2021.109549
• Martin K.D., T. Zhang, T. Lin, A.N. Habowski, R. Zhao, C. Tsai, and W.B. Chrisler, et al. 2021. "Facile one-pot nanoproteomics for label-free proteome profiling of 50-1000 mammalian cells." Journal of Proteome Research 20, no. 9:4452-4461. PNNL-SA-160823. doi:10.1021/acs.jproteome.1c00403
• Satpathy S., K. Krug, P.M. Jean-Beltran, S. Savage, F. Petralia, C. Kumar-Sinha, and Y. Dou, et al. 2021. "A proteogenomic portrait of lung squamous cell carcinoma." Cell 184, no. 16:4348-4371. PNNL-SA-191486. doi:10.1016/j.cell.2021.07.016
• Tsai C., J. Smith, D.S. Eiger, K.D. Martin, T. Liu, R.D. Smith, and T. Shi, et al. 2021. "Mass spectrometry-based proteomics for analysis of hydrophilic phosphopeptides." In Shotgun Proteomics: Methods and Protocols. Methods in Molecular Biology, edited by M. Carrera and J. Mateos. 247-257. New York, New York:Humana Press. PNNL-SA-153327. doi:10.1007/978-1-0716-1178-4_16
• Tsai C., P. Zhang, D. Scholten, K.D. Martin, Y. Wang, R. Zhao, and W.B. Chrisler, et al. 2021. "Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics." Communications Biology 4, no. 1:265. PNNL-SA-150656. doi:10.1038/s42003-021-01797-9
• Wang L., A. Karpova, M.A. Gritsenko, J.E. Kyle, S. Cao, Y. Li, and D. Rykunov, et al. 2021. "Proteogenomic and Metabolomic Characterization of Human Glioblastoma." Cancer Cell 39, no. 4:509-528.e20. PNNL-SA-151124. doi:10.1016/j.ccell.2021.01.006
• Woo J., S.M. Williams, L. Markillie, S. Feng, C. Tsai, V. Aguilera-Vazquez, and R.L. Sontag, et al. 2021. "High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip." Nature Communications 12, no. 1:Art. No. 6246. PNNL-SA-159977. doi:10.1038/s41467-021-26514-2

2020

• Dou Y., E. Kawaler, D.C. Zhou, M.A. Gritsenko, C. Huang, L. Blumenberg, and A. Karpova, et al. 2020. "Proteogenomic Characterization of Endometrial Carcinoma." Cell 180, no. 4:729-748.e26. PNNL-SA-147326. doi:10.1016/j.cell.2020.01.026
• 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
• Hu Y., J. Pan, P. Shah, M. Ao, S.N. Thomas, Y. Liu, and L. Chen, et al. 2020. "Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma." Cell Reports 33, no. 3:108276. PNNL-SA-191200. doi:10.1016/j.celrep.2020.108276
• 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
• 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
• McDermott J.E., O.A. Arshad, V.A. Petyuk, Y. Fu, M.A. Gritsenko, T.R. Clauss, and R.J. Moore, et al. 2020. "Proteogenomic characterization of ovarian HGSC implicates mitotic kinases, replication stress in observed chromosomal instability." Cell Reports Medicine 1, no. 1:Article No. 100004. PNNL-SA-145681. doi:10.1016/j.xcrm.2020.100004
• Petralia F., N. Tignor, B. Reva, M. Koptyra, S. Chowdhury, D. Rykunov, and A. Krek, et al. 2020. "Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer." Cell 183, no. 7:1962-1985. PNNL-SA-155153. doi:10.1016/j.cell.2020.10.044
• 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 & 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
• Williams S.M., A.V. Liyu, C. Tsai, R.J. Moore, D.J. Orton, W.B. Chrisler, and M.J. Gaffrey, et al. 2020. "Automated coupling of nanodroplet sample preparation with liquid chromatography-mass spectrometry for high-throughput single-cell proteomics." Analytical Chemistry 92, no. 15:10588-10596. PNNL-SA-152553. doi:10.1021/acs.analchem.0c01551

2019

• Arshad O.A., V.G. Danna, V.A. Petyuk, P.D. Piehowski, T. Liu, K.D. Rodland, and J.E. McDermott. 2019. "An integrative analysis of tumor proteomic and phosphoproteomic profiles to examine the relationships between kinase activity and phosphorylation." Molecular & Cellular Proteomics 18, no. 8 suppl 1:S26-S36. PNNL-SA-145629. doi:10.1074/mcp.RA119.001540
• Cuesta R., M.A. Gritsenko, V.A. Petyuk, A.K. Shukla, C. Tsai, T. Liu, and J.E. McDermott, et al. 2019. "Phosphoproteome Analysis Reveals Estrogen-ER pathway as a modulator of mTOR activity via DEPTOR." Molecular & Cellular Proteomics 18, no. 8:1607-1618. PNNL-SA-145628. doi:10.1074/mcp.RA119.001506
• 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
• Dou M., G. Clair, C. Tsai, K. Xu, W.B. Chrisler, R.L. Sontag, and R. Zhao, et al. 2019. "High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labelling in a Nanodroplet Sample Preparation Platform." Analytical Chemistry 91, no. 20:13119-13127. PNNL-SA-146297. doi:10.1021/acs.analchem.9b03349
• 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
• Stanfill B.A., L.M. Bramer, T. Liu, and S.M. Akers. 2019. Machine Learning for Rapid Biomarker Discovery via Image-Omic Fusion. PNNL-29450. Richland, WA: Pacific Northwest National Laboratory. Machine Learning for Rapid Biomarker Discovery via Image-Omic Fusion
• Stevens S., T. Liu, F.R. Bahjat, V.A. Petyuk, A.A. Schepmoes, R.L. Sontag, and M.A. Gritsenko, et al. 2019. "Preconditioning in the Rhesus Macaque Induces a Proteomic Signature Following Cerebral Ischemia that Is Associated with Neuroprotection." Translational Stroke Research 10, no. 4:440-448. PNWD-SA-10567. doi:10.1007/s12975-018-0670-7
• Stevens S.L., T. Liu, F.R. Bahjat, V.A. Petyuk, A.A. Schepmoes, R.L. Sontag, and M.A. Gritsenko, et al. 2019. "Preconditioning in the Rhesus Macaque Induces a Proteomic Signature Following Cerebral Ischemia That Is Associated With Neuroprotection." Translational Stroke Research 10, no. 4:440-448. PNNL-SA-153569. doi:10.1007/s12975-018-0670-7
• 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
• Vasaikar S., C. Huang, X. Wang, V.A. Petyuk, S. Savage, B. Wen, and Y. Dou, et al. 2019. "Proteogenomic analysis of human colon cancer reveals new therapeutic opportunities." Cell 177, no. 4:1035-1049. PNNL-SA-137631. doi:10.1016/j.cell.2019.03.030
• 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

2018

• 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
• Garabedian A., P. Benigni, C. Ramirez, E.M. Baker, T. Liu, R.D. Smith, and F. Fernandez-Lima. 2018. "Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS." Journal of the American Society for Mass Spectrometry 29, no. 5:817-826. PNNL-SA-129610. doi:10.1007/s13361-017-1787-8
• Hosseini M.M., S.E. Kurtz, S. Abdelhamed, S. Mahmood, M.A. Davare, A. Kaempf, and J. Elferich, et al. 2018. "Inhibition of interleukin-1 receptor-associated kinase-1 is a therapeutic strategy for acute myeloid leukemia subtypes." Leukemia 32, no. 11:2374-2387. PNNL-SA-137772. doi:10.1038/s41375-018-0112-2
• Mertins P., L.C. Tang, K. Krug, D.J. Clark, M.A. Gritsenko, L. Chen, and K. Clauser, et al. 2018. "Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry." Nature Protocols 13, no. 7:1632-1661. PNNL-SA-137930. doi:10.1038/s41596-018-0006-9
• Park J., P.D. Piehowski, C.S. Wilkins, M. Zhou, J.A. Mendoza, G.M. Fujimoto, and B.C. Gibbons, et al. 2018. "Author Correction: Informed-Proteomics: open-source software package for top-down proteomics." Nature Methods 15. PNNL-SA-162101. doi:10.1038/s41592-018-0040-0
• 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

2017

• 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
• Park J., P.D. Piehowski, C.S. Wilkins, M. Zhou, J.A. Mendoza, G.M. Fujimoto, and B.C. Gibbons, et al. 2017. "Informed-Proteomics: Open Source Software Package for Top-down Proteomics." Nature Methods 14, no. 9:909-914. PNNL-SA-120171. doi:10.1038/nmeth.4388
• 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
• Wang S., F. Yang, V.A. Petyuk, A.K. Shukla, M.E. Monroe, M.A. Gritsenko, and K.D. Rodland, et al. 2017. "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease." Journal of Pathology 243, no. 1:78-88. PNNL-SA-119241. doi:10.1002/path.4929
• Zhou J., L. Chen, B. Zhang, Y. Tian, T. Liu, S.N. Thomas, and L. Chen, et al. 2017. "Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues." Journal of Proteome Research 16, no. 12:4523-4530. PNNL-SA-105677. doi:10.1021/acs.jproteome.7b00362

2016

• 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 & Cellular Proteomics 15, no. 12:3694-3705. PNNL-SA-118308. doi:10.1074/mcp.M116.061143
• Gritsenko M.A., Z. Xu, T. Liu, and R.D. 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, edited by S Sechi. 237-247. New York, New York:Springer. PNNL-SA-107351.
• Hatakeyama H., S.Y. Wu, Y.A. Lyons, S. Pradeep, W. Wang, Q. Huang, and K.A. Court, et al. 2016. "Role of CTGF in Sensitivity to Hyperthermia in Ovarian and Uterine Cancers." Cell Reports 17, no. 6:1621-1631. PNNL-SA-120868. doi:10.1016/j.celrep.2016.10.020
• 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
• Ruggles K., Z. Tang, Z. Tang, X. Wang, H. Grover, M. Askenazi, and J. Teubl, et al. 2016. "An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer." Molecular & Cellular Proteomics 15, no. 3:1060-1071. PNNL-SA-105676. doi:10.1074/mcp.M115.056226
• 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
• Tabb D.L., X. Wang, S.A. Carr, K. Clauser, P. Mertins, M.C. Chambers, and J.D. Holman, et al. 2016. "Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts." Journal of Proteome Research 15, no. 3:691-706. PNNL-SA-113210. doi:10.1021/acs.jproteome.5b00859
• 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 Proteomics 13, no. 1:99-114. PNNL-SA-113659. doi:10.1586/14789450.2016.1122529
• Whiteaker J.R., G. Halusa, A.N. Hoofnagle, V. Sharma, B. MacLean, P. Yan, and J. Wrobel, et al. 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, edited by S Sechi. 223-263. New York, New York:Springer. PNNL-SA-110086. doi:10.1007/978-1-4939-3524-6_13
• Wu C., J. Duan, T. Liu, R.D. Smith, and W. Qian. 2016. "Contributions of Immunoaffinity Chromatography to Deep Proteome Profiling of Human Biofluids." Journal of Chromatography B 1021. PNNL-SA-112289. doi:10.1016/j.jchromb.2016.01.015
• Zhang H., T. Liu, Z. Zhang, S.H. Payne, B. Zhang, J.E. McDermott, and J. Zhou, et al. 2016. "Integrated proteogenomic characterization of human high grade serous ovarian cancer." Cell 166, no. 3:755-765. PNNL-SA-107151. doi:10.1016/j.cell.2016.05.069

2015

• 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
• Wang H., Y. Yang, Y. Li, B. Bai, X. Wang, H. Tan, and T. Liu, et al. 2015. "Systematic Optimization of Long Gradient Chromatography Mass Spectrometry for Deep Analysis of Brain Proteome." Journal of Proteome Research 14, no. 2:829-838. PNNL-SA-105913. doi:10.1021/pr500882h
• Wu C., M.E. Monroe, Z. Xu, G.W. Slysz, S.H. Payne, K.D. Rodland, and T. Liu, et al. 2015. "An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics." Journal of the American Society for Mass Spectrometry 26, no. 12:2002-2008. PNNL-SA-108032. doi:10.1007/s13361-015-1169-z
• Wu C., T. Liu, E.S. Baker, K.D. Rodland, and R.D. Smith. 2015. "Mass spectrometry for biomarker development." In General Methods in Biomarker Research and their Applications. Biomarkers in Disease: Methods, Discoveries and Applications, edited by V Preedy and V Patel. 17-48. Heidelberg:Springer. PNNL-SA-97608.
• 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

• Carr S.A., S.E. Abbateillo, B.L. Ackermann, C.H. Borchers, B. Domon, E.W. Deutsch, and R. Grant, et al. 2014. "Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach." Molecular & Cellular Proteomics 13, no. 3:907-917. PNNL-SA-102320. doi:10.1074/mcp.M113.036095
• Guo J., M.J. Gaffrey, D. Su, T. Liu, D.G. Camp, R.D. 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, no. 1:64-75. PNNL-SA-96060. doi:10.1038/nprot.2013.161
• 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
• Mertins P., F. Yang, T. Liu, D. Mani, V.A. Petyuk, M. Gillette, and K. Clauser, et al. 2014. "Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels." Molecular & Cellular Proteomics 13, no. 7:1690-1704. PNNL-SA-98702. doi:10.1074/mcp.M113.036392
• 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
• Wang S., F. Yang, D.G. Camp, K.D. Rodland, W. Qian, T. Liu, and R.D. Smith. 2014. "Proteomic Approaches for Site-specific O-GlcNAcylation Analysis." Bioanalysis 6, no. 19:2571-2580. PNNL-SA-102529. doi:10.4155/bio.14.239
• Whiteaker J.R., G. Halusa, A.N. Hoofnagle, V. Sharma, B. MacLean, P. Yan, and J. Wrobel, et al. 2014. "CPTAC Assay Portal: a repository of targeted proteomic assays." Nature Methods 11, no. 7:703-704. PNNL-SA-103950. doi:10.1038/nmeth.3002
• Woo S., S. Cha, S. Na, C. Guest, T. Liu, R.D. Smith, and K.D. Rodland, et al. 2014. "Proteogenomic strategies for identification of aberrant cancer peptides using large-scale Next Generation Sequencing data." Proteomics 14, no. 23-24:2719-2730. PNNL-SA-105664. doi:10.1002/pmic.201400206
• 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

• Finnerty C.C., M.G. Jeschke, W. Qian, A. Kaushal, W. Xiao, T. Liu, and M.A. Gritsenko, et al. 2013. "DETERMINATION OF BURN PATIENT OUTCOME BY LARGE-SCALE QUANTITATIVE DISCOVERY PROTEOMICS." Critical Care Medicine 41, no. 6:1421-1434. PNWD-SA-9845. doi:10.1097/CCM.0b013e31827c072e
• Schutzer S.E., T.E. Angel, T. Liu, A.A. Schepmoes, F. Xie, J.P. Bergquist, and L. Vecsei, et al. 2013. "Gray Matter Is Targeted in First-Attack Multiple Sclerosis." PLoS One 8, no. 9:E6617. PNNL-SA-98547. doi:10.1371/journal.pone.0066117
• 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

2012

• Baker E.S., T. Liu, V.A. Petyuk, K.E. Burnum-Johnson, Y.M. Ibrahim, G.A. Anderson, and R.D. Smith. 2012. "Mass Spectrometry for Translational Proteomics: Progress and Clinical Implications." Genome Medicine 4. PNNL-SA-86783. doi:10.1186/gm364
• Chauvin T., F. Xie, T. Liu, C.D. Nicora, F. Yang, D.G. Camp, and R.D. Smith, et al. 2012. "A Systematic Analysis of a Deep Mouse Epididymal Sperm Proteome." Biology of Reproduction 87, no. 6:Article No. 141. PNNL-SA-90200. doi:10.1095/biolreprod.112.104208
• Hu Z., E.R. Browne, T. Liu, T.E. Angel, P.C. Ho, and E. Chun Yong Chan. 2012. "Metabonomic Profiling of TASTPM Transgenic Alzheimer's Disease Mouse Model." Journal of Proteome Research 11, no. 12:5903-5913. PNNL-SA-90706. doi:10.1021/pr300666p
• 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., 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
• Wang L., U.K. Aryal, Z. Dai, A.C. Mason, M.E. Monroe, Z. Tian, and J. Zhou, et al. 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, no. 1:143-56. PNNL-SA-82556. doi:10.1021/pr200916k
• Waters K.M., T. Liu, R.D. Quesenberry, A.R. Willse, S. Bandyopadhyay, L.E. Kathmann, and T.J. Weber, et al. 2012. "Network Analysis of Epidermal Growth Factor Signaling using Integrated Genomic, Proteomic and Phosphorylation Data." PLoS One 7, no. 3:Article No. e34515. PNNL-SA-85737. doi:10.1371/journal.pone.0034515
• 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

2011

• Hossain M., D.T. Kaleta, E.W. Robinson, T. Liu, R. Zhao, J.S. Page, and R.T. Kelly, et al. 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, no. 2. PNNL-SA-70166. doi:10.1074/mcp.M000062-MCP201
• 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
• Schoenherr R.M., K.S. Kelly-Spratt, C. Lin, J.R. Whiteaker, T. Liu, T. Holzman, and I. Coleman, et al. 2011. "Proteome and Transcriptome Profiles of a Her2/Neu-driven Mouse Model of Breast Cancer." Proteomics - Clinical Applications 5, no. 3-4:179-188. PNNL-SA-72407. doi:10.1002/prca.201000037
• Schutzer S.E., T.E. Angel, T. Liu, A.A. Schepmoes, T.R. Clauss, J.N. Adkins, and D.G. Camp, et al. 2011. "Distinct Cerebrospinal Fluid Proteomes Differentiate Post-Treatment Lyme Disease from Chronic Fatigue Syndrome." PLoS One 6, no. 2:Article No. e17287. PNWD-SA-9128. doi:10.1371/journal.pone.0017287
• Wang Y., F. Yang, M.A. Gritsenko, Y. Wang, T.R. Clauss, T. Liu, and Y. Shen, et al. 2011. "Reversed-Phase Chromatography with Multiple Fraction Concatenation Strategy for Proteome Profiling of Human MCF10A Cells." Proteomics 11, no. 10:2019-2026. PNNL-SA-75439. doi:10.1002/pmic.201000722
• Xie F., T. Liu, W. Qian, V.A. Petyuk, and R.D. Smith. 2011. "Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics." Journal of Biological Chemistry 286, no. 29:25443-25449. PNNL-SA-76123.
• Zhang H., K.E. Burnum, M.L. Luna, B.O. Petritis, J. Kim, W. Qian, and R.J. Moore, et al. 2011. "Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size." Proteomics 11, no. 23:4569-4577. PNNL-SA-74159. doi:10.1002/pmic.201100037

2010

• Schutzer S.E., T. Liu, B. Natelson, T.E. Angel, A.A. Schepmoes, S.O. Purvine, and K.K. Hixson, et al. 2010. "Establishing the Proteome of Normal Human Cerebrospinal Fluid." PLoS One 5, no. 6:e10980-. PNWD-SA-8931. doi:10.1371/journal.pone.0010980
• Shen Y., N. Tolic, T. Liu, R. Zhao, B.O. Petritis, M.A. Gritsenko, and D.G. Camp, et al. 2010. "Blood Peptidome-Degradome Profile of Breast Cancer." PLoS One 5, no. 10:Article No.: e13133. PNNL-SA-70095. doi:10.1371/journal.pone.0013133
• Shen Y., T. Liu, N. Tolic, B.O. Petritis, R. Zhao, R.J. Moore, and S.O. Purvine, et al. 2010. "A strategy for degradomic-peptidomic analysis of the human blood plasma." Journal of Proteome Research 9, no. 5:2339-2346. PNNL-SA-71375. doi:10.1021/pr901083m

2009

• Qian W., T. Liu, V.A. Petyuk, M.A. Gritsenko, B.O. Petritis, A.D. Polpitiya, and A. Kaushal, et al. 2009. "Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an O-18-Labeled “Universal” Reference Sample." Journal of Proteome Research 8, no. 1:290-299. PNNL-SA-57317.

2008

• Pertz O.C., Y. Wang, F. Yang, W. Wang, l.J. gay, M.A. Gritsenko, and T.R. Clauss, et al. 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, no. 6:1931-1936. PNNL-SA-58516. doi:10.1073/pnas.0706545105
• Qian W., D.T. Kaleta, B.A. Ogata, H. Jiang, T. Liu, X. Zhang, and H.M. Mottaz, et al. 2008. "Enhanced Detection of Low Abundant Human Plasma Proteins using a Tandem IgY12-SuperMix Immunoaffinity Separation Strategy." Molecular & Cellular Proteomics. MCP 7, no. 10:1963-1973. PNWD-SA-8062. doi:10.1074/mcp.M800008-MCP200
• Rogers S., M. Girolami, M. Girolami, W. Kolch, K.M. Waters, T. Liu, and B.D. Thrall, et al. 2008. "Investigating the Correspondence Between Transcriptomic and Proteomic Expression Profiles Using Coupled Cluster Models." Bioinformatics 24, no. 24:2894-2900. PNNL-SA-61286. doi:10.1093/bioinformatics/btn553

2007

• Chan E.Y., W. Qian, D.L. Diamond, T. Liu, M.A. Gritsenko, M.E. Monroe, and D.G. Camp, et al. 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, no. 14:7571-7583. PNWD-SA-7667.
• Liu T., M.E. Belov, N. Jaitly, W. Qian, and R.D. Smith. 2007. "Accurate Mass Measurements in Proteomics." Chemical Reviews 107, no. 8:3621-3653. PNNL-SA-52331. doi:10.1021/cr068288j
• Liu T., W. Qian, D.G. Camp, and R.D. 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. 107-24. Totowa, New Jersey:Humana Press. PNNL-SA-44833.
• Whiteaker J.R., H. Zhang, J.K. Eng, R. Fang, B.D. Piening, L. Feng, and T.D. lorentzen, et al. 2007. "Head-to-Head Comparison of Serum Fractionation Techniques." Journal of Proteome Research 6, no. 2:828-836. PNWD-SA-7568. doi:10.1021/pr0604920

2006

• Liu T., W. Qian, H.M. Mottaz, M.A. Gritsenko, A.D. Norbeck, R.J. Moore, and S.O. Purvine, et al. 2006. "Evaluation of Multi-Protein Immunoaffinity Subtraction for Plasma Proteomics and Candidate Biomarker Discovery Using Mass Spectrometry." Molecular & Cellular Proteomics. MCP 5, no. 11:2167-2174. PNWD-SA-7363.
• Liu T., W. Qian, M.A. Gritsenko, W. Xiao, L.L. Moldawer, A. Kaushal, and M.E. Monroe, et al. 2006. "High Dynamic Range Characterization of the Trauma Patient Plasma Proteome." Molecular & Cellular Proteomics. MCP 5, no. 10:1899-1913. PNWD-SA-7271. doi:10.1074/mcp.M600068-MCP200
• Qian W., J.M. Jacobs, T. Liu, D.G. Camp, and R.D. Smith. 2006. "Advances and Challenges in Liquid Chromatography-Mass Spectrometry-Based Proteomics Profiling for Clinical Applications." Molecular & Cellular Proteomics. MCP 5, no. 10:1727-1744. PNWD-SA-7399. doi:10.1074/mcp.M600162-MCP200
• Wang H.H., W. Qian, M.H. Chin, V.A. Petyuk, R.C. Barry, T. Liu, and M.A. Gritsenko, et al. 2006. "Characterization of the Mouse Brain Proteome Using Global Proteomic Analysis Complemented with Cysteinyl-Peptide Enrichment." Journal of Proteome Research 5, no. 2:361-369. PNNL-SA-46752.

2005

• Jacobs J.M., J.N. Adkins, W. Qian, T. Liu, Y. Shen, D.G. Camp, and R.D. Smith. 2005. "Utilizing human blood plasma for proteomic biomarker discovery." Journal of Proteome Research 4, no. 4:1073-1085. PNWD-SA-6880. doi:10.1021/pr0500657
• Liu T., W. Qian, M.A. Gritsenko, D.G. Camp, M.E. Monroe, R.J. Moore, and R.D. Smith. 2005. "Human Plasma N-Glycoproteome Analysis by Immunoaffinity Subtraction, Hydrazide Chemistry, and Mass Spectrometry." Journal of Proteome Research 4, no. 6:2070-2080. PNNL-SA-44967.
• Liu T., W. Qian, W.U. Chen, J.M. Jacobs, R.J. Moore, D.J. Anderson, and M.A. Gritsenko, et al. 2005. "Improved Proteome Coverage by Using High Efficiency Cysteinyl-peptide Enrichment: The Human Mammary Epithelial Cell Proteome." Proteomics 5, no. 5:1263-1273. PNNL-SA-42468.
• Qian W., M.E. Monroe, T. Liu, J.M. Jacobs, G.A. Anderson, Y. Shen, and R.J. Moore, et al. 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, no. 5:700-709. PNNL-SA-44302.
• Qian W., T. Liu, M.E. Monroe, E.F. Strittmatter, J.M. Jacobs, L.J. Kangas, and K. Petritis, et al. 2005. "Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis: The Human Proteome." Journal of Proteome Research 4, no. 1:53-62. PNNL-SA-42815.

2004

• Liu T., W. Qian, E.F. Strittmatter, D.G. Camp, G.A. Anderson, B.D. Thrall, and R.D. Smith. 2004. "High throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology." Analytical Chemistry 76, no. 18:5345-5353. PNWD-SA-6477.