Staff information

PNNL Publications

2017

• Li M, W Qian, Y Gao, L Shi, and C Liu. 2017. "Functional Enzyme-based Approach for Linking Microbial Community Functions with Biogeochemical Process Kinetics." Environmental Science & Technology 51(20):11848-11857.  doi:10.1021/acs.est.7b03158
• Li M, Y Gao, W Qian, L Shi, Y Liu, WC Nelson, CD Nicora, CT Resch, CJ Thompson, S Yan, JK Fredrickson, JM Zachara, and C Liu. 2017. "Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes." Environmental Microbiology Reports 9(5):512-521.  doi:10.1111/1758-2229.12558
• Nie S, T Shi, TL Fillmore, AA Schepmoes, HM Brewer, Y Gao, E Song, H Wang, KD Rodland, W Qian, RD Smith, and T Liu. 2017. "Deep-dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues." Analytical Chemistry 89(17):9139-9146.  doi:10.1021/acs.analchem.7b01878
• Song E, Y Gao, C Wu, T Shi, S Nie, TL Fillmore, AA Schepmoes, MA Gritsenko, W Qian, RD Smith, KD Rodland, and T Liu. 2017. "Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer." Scientific Data 4:170091.  doi:10.1038/sdata.2017.91
• Wang H, CE Barbieri, J He, Y Gao, T Shi, C Wu, AA Schepmoes, TL Fillmore, SS Chae, D Huang, JM Mosquera, WJ Qian, RD Smith, S Srivastava, J Kagan, DG Camp, II, KD Rodland, M Rubin, and T Liu. 2017. "Quantification of Mutant SPOP Proteins in Prostate Cancer Using Mass Spectrometry-Based Targeted Proteomics." Journal of Translational Medicine 15:Article No. 175.  doi:10.1186/s12967-017-1276-7
• Yang L, T Stewart, M Shi, G Pottiez, R Dator, R Wu, P Aro, RJ Schuster, C Ginghina, C Pan, Y Gao, W Qian, CP Zabetian, SC Hu, JF Quinn, MD, and J Zhang. 2017. "An alpha-synuclein MRM assay with diagnostic potential for Parkinson’s disease and monitoring disease progression." Proteomics - Clinical Applications 11(7-8):Article No. 1700045.  doi:10.1002/prca.201700045

2016

• Guo X, TL Fillmore, Y Gao, and K Tang. 2016. "Capillary Electrophoresis-nanoelectrospray Ionization-selected Reaction Monitoring Mass Spectrometry Via A True Sheathless Metal-coated Emitter Interface For Robust And High Sensitivity Sample Quantification." Analytical Chemistry 88(8):4418-4425.  doi:10.1021/acs.analchem.5b04912
• Ho ME, SI Quek, LD True, R Seiler, A Fleischmann, L Bagryanova, SR Kim, D Chia, L Goodglick, Y Shimizu, CJ Rosser, Y Gao, and AY Liu. 2016. "Bladder cancer cells secrete while normal bladder cells express but do not secrete AGR2." Oncotarget 7(13):15747-15756.  doi:10.18632/oncotarget.7400
• 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
• Nielson C, K Jones, RF Chun, JM Jacobs, Y Wang, M Hewison, JS Adams, C Swanson, C Lee, D Vanderschueren, A Prentice, RD Smith, T Shi, Y Gao, JM Zmuda, J Lapidus, JA Cauley, R Bouillon, I Shoenmakers, and ES Orwoll. 2016. "Role of Assay Type in Determining Free 25-Hydroxyvitamin D Levels in Diverse Populations." The New England Journal of Medicine 374(17):1695-1696.  doi:10.1056/NEJMc1513502
• Nielson C, K Jones, RF Chun, JM Jacobs, Y Wang, M Hewison, JS Adams, C Swanson, C Lee, D Vanderschueren, S Pauwels, A Prentice, RD Smith, T Shi, Y Gao, AA Schepmoes, JM Zmuda, J Lapidus, JA Cauley, R Bouillon, I Schoenmakers, and ES Orwoll. 2016. "Free 25-Hydroxyvitamin D: Impact of Vitamin D Binding Protein Assays on Racial-Genotypic Associations." Journal of Clinical Endocrinology and Metabolism 101(5):2226-2234.  doi:10.1210/jc.2016-1104
• Shi T, M Niepel, JE McDermott, Y Gao, CD Nicora, WB Chrisler, LM Markillie, VA Petyuk, RD Smith, KD Rodland, P Sorger, W Qian, and HS Wiley. 2016. "Conservation of Protein Abundance Patterns Reveals the Regulatory Architecture of the of the EGFR-MAPK Pathway." Science Signaling 9(436):rs6.  doi:10.1126/scisignal.aaf0891
• Sigdel TK, Y Gao, J He, A Wang, CD Nicora, TL Fillmore, T Shi, BJM Webb-Robertson, RD Smith, W Qian, O Salvatierra, DG Camp, II, and M Sarwal. 2016. "Mining the Human Urine Proteome for Monitoring Renal Transplant Injury ." Kidney International 89(6):1244-1252.  doi:10.1016/j.kint.2015.12.049

2015

• 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

2014

• Shi T, Y Gao, MJ Gaffrey, CD Nicora, TL Fillmore, WB Chrisler, MA Gritsenko, C Wu, J He, KJ Bloodsworth, R Zhao, DG Camp, II, T Liu, KD Rodland, RD Smith, HS Wiley, and W Qian. 2014. "Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells without Affinity Enrichment." Analytical Chemistry 87(2):1103-1110.  doi:10.1021/ac503797x
• Shi T, Y Gao, SI Quek, TL Fillmore, CD Nicora, D Su, R Zhao, KD Rodland, T Liu, RD Smith, DW Chan, DG Camp, II, AY Liu, and W Qian. 2014. "A highly sensitive targeted mass spectrometric assay for quantification of low-abundance AGR2 in human urine and serum." Journal of Proteome Research 13(2):875-882.  doi:10.1021/pr400912c
• Wu C, T Shi, JN Brown, J He, Y Gao, TL Fillmore, AK Shukla, RJ Moore, DG Camp, II, KD Rodland, W Qian, T Liu, and RD Smith. 2014. "Expediting SRM assay development for large-scale targeted proteomics experiments." Journal of Proteome Research 13(10):4479-87.  doi:10.1021/pr500500d

2013

• Shi T, TL Fillmore, Y Gao, R Zhao, J He, AA Schepmoes, CD Nicora, C Wu, JL Chambers, RJ Moore, J Kagan, S Srivastava, AY Liu, KD Rodland, T Liu, DG Camp, II, RD Smith, and W Qian. 2013. "Long-Gradient Separations Coupled with Selected Reaction Monitoring for Highly Sensitive, Large Scale Targeted Protein Quantification in a Single Analysis." Analytical Chemistry 85(19):9196-9203.  doi:10.1021/ac402105s
• Shi T, X Sun, Y Gao, TL Fillmore, AA Schepmoes, R Zhao, J He, RJ Moore, J Kagan, KD Rodland, T Liu, AY Liu, RD Smith, K Tang, DG Camp, II, and W Qian. 2013. "Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion." Journal of Proteome Research 12(7):3353-3361.  doi:10.1021/pr400178v
• Zhou J, RK Krovvidi, Y Gao, H Gao, BO Petritis, A De, C Miller-Graziano, PE Bankey, VA Petyuk, CD Nicora, TRW Clauss, RJ Moore, T Shi, JN Brown, A Kaushal, W Xiao, RW Davis, RV Maier, RG Tompkins, W Qian, DG Camp, II, and RD Smith. 2013. "Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling." Proteomics - Clinical Applications 7(7-8):571-583.  doi:10.1002/prca.201200109