Wei-Jun Qian

Bioanalytical Chemist, Lab Fellow

Biography

Wei-Jun Qian is a bioanalytical chemist whose research centers primarily on the development and applications of mass spectrometry-based approaches to better quantify the dynamic changes in protein abundances and protein post-translational modifications in biological and clinical applications. Qian is currently a staff scientist in the Integrative Omics group in the Biological Sciences Division, where he has worked since 2002. Qian's current research involves the development of chemical proteomic approaches for site-specific quantification of cysteine-based redox modifications and more sensitive selected reaction monitoring-based targeted quantification techniques with applications in pancreatic islets, diabetes, and oxidative stress-related disease areas. In addition to research, he is actively involved in training and mentoring postdoctoral researchers and intern students.

Education

PhD in Bioanalytical Chemistry, University of Florida
BS in Chemistry, Nanjing University

Awards and Recognitions

Presidential Early Career Award for Scientists and Engineers, 2011
Director's New Innovator Award, National Institutes of Health, 2009

Publications

2021

Xu Z., C. Pan, X. Li, N. Hao, T. Zhang, M.J. Gaffrey, and Y. Pu, et al. 2021. "Enhancement of Polyhydroxyalkanoate Production by Co-feeding Lignin Derivatives with Glycerol in Pseudomonas putida KT2440." Biotechnology for Biofuels 14, no. 1:Article No. 11. PNNL-SA-157585. doi:10.1186/s13068-020-01861-2
Li X., N.J. Day, S. Feng, M.J. Gaffrey, T. Lin, V.L. Paurus, and M.E. Monroe, et al. 2021. "Mass spectrometry-based direct detection of multiple types of protein thiol modifications in pancreatic beta cells under endoplasmic reticulum stress." Redox Biology 46. PNNL-SA-163313. doi:10.1016/j.redox.2021.102111
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
Cao X., X. Pan, S.P. Couvillion, T. Zhang, C. Tamez, L.M. Bramer, and J. White, et al. 2021. "Fate, cytotoxicity and cellular metabolomic impact of ingested nanoscale carbon dots using simulated digestion and a triculture small intestinal epithelial model." NanoImpact 23. PNNL-SA-166081. doi:10.1016/j.impact.2021.100349
Rodriguez-Calvo T., Y. Chien, B. Verchere, L. Haataja, P. Arvan, P. Leete, and S.J. Richardson, et al. 2021. "Altered ß-cell Prohormone Processing and Secretion in Type 1 Diabetes." Diabetes 70, no. 5:1038-1050. PNNL-SA-158708. doi:10.2337/dbi20-0034
Fulcher J.M., A. Makaju, R.J. Moore, M. Zhou, D.A. Bennett, P.L. De Jager, and W. Qian, et al. 2021. "Enhancing top-down proteomics of brain tissue with FAIMS." Journal of Proteome Research 20, no. 5:2780-2795. PNNL-SA-159227. doi:10.1021/acs.jproteome.1c00049
Petyuk V.A., L. Yu, H.M. Olson, F. Yu, G. Clair, W. Qian, and J.M. Shulman, et al. 2021. "Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss." Journal of Proteome Research 20, no. 5:2266-2282. PNNL-SA-153429. doi:10.1021/acs.jproteome.0c00747
Gaffrey M.J., N.J. Day, X. Li, and W. Qian. 2021. "Resin Assisted Capture Coupled with Isobaric Tandem Mass Tag Labeling for Multiplexed Quantification of Protein Thiol Oxidation." Journal of Visualized Experiments (JoVE). PNNL-SA-162161. doi:10.3791/62671
Hutchinson C.M., J.A. Sanford, J.R. Hansen, M.A. Gritsenko, K.D. Rodland, P.D. Piehowski, and W. Qian, et al. 2021. "Assessment of TMT labeling efficiency in large-scale quantitative proteomics: the critical effect of sample pH." ACS Omega 6, no. 19:12660-12666. PNNL-SA-158792. doi:10.1021/acsomega.1c00776
Zhang T., M.J. Gaffrey, X. Li, and W. Qian. 2021. "Characterization of cellular oxidative stress response by stoichiometric redox proteomics." American Journal of Physiology. Cell Physiology 320, no. 2:C182-C194. PNNL-SA-151503. doi:10.1152/ajpcell.00040.2020
Day N.J., M.J. Gaffrey, and W. Qian. 2021. "Stoichiometric Thiol Redox Proteomics for Quantifying Cellular Responses to Perturbations." Antioxidants 10, no. 3:499. PNNL-SA-160301. doi:10.3390/antiox10030499
Ni X., X. Li, T. Shen, W. Qian, and M. Xian. 2021. "A Sweet H2S/H2O2 Dual Release System and Specific Protein S-Persulfidation Mediated by Thioglucose/Glucose Oxidase." Journal of the American Chemical Society 143, no. 33:13325 - 13332. PNNL-SA-164769. doi:10.1021/jacs.1c06372
Swensen A.C., J. He, A.C. Fang, Y. Ye, C.D. Nicora, T. Shi, and A.Y. Liu, et al. 2021. "A comprehensive urine proteome database generated from patients with various renal conditions and prostate cancer." Frontiers in Medicine 8. PNNL-SA-152473. doi:10.3389/fmed.2021.548212
Wang J., S. Kim, E. House, H.M. Olson, C.J. Johnston, D. Chalupa, and E. Hernady, et al. 2021. "Repetitive diacetyl vapor exposure promotes ubiquitin proteasome stress and precedes bronchiolitis obliterans pathology." Archives of Toxicology 95, no. 7:2469–2483. PNNL-SA-159891. doi:10.1007/s00204-021-03076-2
Nakayasu E.S., M.A. Gritsenko, P.D. Piehowski, Y. Gao, D.J. Orton, A.A. Schepmoes, and T.L. Fillmore, et al. 2021. "Tutorial: best practices and considerations for mass spectrometry-based protein biomarker discovery and validation." Nature Protocols 16. PNNL-SA-154632. doi:10.1038/s41596-021-00566-6
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
Li X., Z. Xu, J.R. Cort, W. Qian, and B. Yang. 2021. "Lipid production from non-sugar compounds in pretreated lignocellulose hydrolysates by Rhodococcus jostii RHA1." Biomass & Bioenergy 145. PNNL-SA-153203. doi:10.1016/j.biombioe.2021.105970

2020

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
Wang J., T. Zhang, C.J. Johnston, S. Kim, M.J. Gaffrey, D. Chalupa, and G. Feng, et al. 2020. "Protein thiol oxidation in the rat lung following e-cigarette exposure." Redox Biology 37. PNNL-SA-154549. doi:10.1016/j.redox.2020.101758
Cao X., T. Zhang, G.M. Deloid, M.J. Gaffrey, K.K. Weitz, B.D. Thrall, and W. Qian, et al. 2020. "Cytotoxicity and cellular proteome impact of cellulose nanocrystals using simulated digestion and an in vitro small intestinal epithelium cellular model." NanoImpact 20. PNNL-SA-157451. doi:10.1016/j.impact.2020.100269
Duan J., T. Zhang, M.J. Gaffrey, K.K. Weitz, R.J. Moore, X. Li, and M. Xian, et al. 2020. "Stochiometric Quantification of the Thiol Redox Proteome of Macrophages Reveals Subcellular Compartmentalization and Susceptibility to Oxidative Perturbations." Redox Biology 36. PNNL-SA-153520. doi:10.1016/j.redox.2020.101649
Chiao Y., H. Zhang, M. Sweetwyne, J. Whitson, Y. Ting, N. Basisty, and L. Pino, et al. 2020. "Late-life restoration of mitochondrial function reverses cardiac dysfunction in old mice." eLife 9. PNNL-SA-150324. doi:10.1101/2020.01.02.893008
Sigdel T.K., P.D. Piehowski, S. Roy, J. LIberto, J.R. Hansen, A.C. Swensen, and R. Zhao, et al. 2020. "Near-Single-Cell Proteomics Profiling of the Proximal Tubular and Glomerulus of the Normal Human Kidney." Frontiers in Medicine 7. PNNL-SA-145047. doi:10.3389/fmed.2020.00499
Zhang Y., Z. Ouyang, W. Qian, R.D. Smith, W. Wong, and R.W. Davis. 2020. "Meta-analysis of peptides to detect protein significance." Statistics and It's Interface 13, no. 4:465-474. PNNL-SA-152554. doi:10.4310/sii.2020.v13.n4.a4
Shin S., J. Hong, Y. Na, M. Lee, W. Qian, V.N. Kim, and J. Kim. 2020. "Development of Multiplexed Immuno-N-Terminomics to Reveal the Landscape of Proteolytic Processing in Early Embryogenesis of Drosophila melanogaster." Analytical Chemistry 92, no. 7:4926-4934. PNNL-SA-149241. doi:10.1021/acs.analchem.9b05035
Cao X., T. Zhang, G.M. DeLoid, M.J. Gaffrey, K.K. Weitz, B.D. Thrall, and W. Qian, et al. 2020. "Evaluation of the cytotoxic and cellular proteome impacts of food-grade TiO2 (E171) using simulated gastrointestinal digestions and a tri-culture small intestinal epithelial model." NanoImpact 17. PNNL-SA-147195. doi:10.1016/j.impact.2019.100202
Zhang T., M.J. Gaffrey, M.E. Monroe, D.G. Thomas, K.K. Weitz, P.D. Piehowski, and V.A. Petyuk, et al. 2020. "Block design with common reference samples enables robust large-scale label-free quantitative proteome profiling." Journal of Proteome Research 19, no. 7:2863–2872. PNNL-SA-151164. doi:10.1021/acs.jproteome.0c00310
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
Sanford J.A., C.D. Nogiec, M.E. Lindholm, J.N. Adkins, D. Amar, S. Dasari, and J.K. Drugan, et al. 2020. "Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise." Cell 181, no. 7:1464-1474. PNNL-SA-155782. doi:10.1016/j.cell.2020.06.004
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
Nakayasu E.S., F. Syed, S. Tersey, M.A. Gritsenko, H.D. Mitchell, C. Chan, and J. Turatsinze, et al. 2020. "Comprehensive proteomics analysis of stressed human islets identifies GDF15 as a target for type 1 diabetes intervention." Cell Metabolism 31, no. 2:363-374.e6. PNNL-SA-150166. doi:10.1016/j.cmet.2019.12.005
Wang X., A.C. Swensen, T. Zhang, P.D. Piehowski, M.J. Gaffrey, M.E. Monroe, and Y. Zhu, et al. 2020. "Accurate Identification of Deamidation and Citrullination from Global Shotgun Proteomics Data Using a Dual-search Delta Score Strategy." Journal of Proteome Research 19, no. 4:1863-1872. PNNL-SA-149222. doi:10.1021/acs.jproteome.9b00766
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
Zhang T., M.J. Gaffrey, D.G. Thomas, T.J. Weber, B.M. Hess, K.K. Weitz, and P.D. Piehowski, et al. 2020. "A proteome-wide assessment of the oxidative stress paradigm for metal and metal-oxide nanomaterials in human macrophages." NanoImpact 17. PNNL-SA-147217. doi:10.1016/j.impact.2019.100194

2019

Campbell M.D., J. Duan, A.T. Samuelson, M.J. Gaffrey, G.E. Merrihew, J.D. Egertson, and L. Wang, et al. 2019. "Improving mitochondrial function with SS-31 reverses age-related redox stress and improves exercise tolerance in aged mice." Free Radical Biology & Medicine 134. PNNL-SA-140379. doi:10.1016/j.freeradbiomed.2018.12.031
Dirice E., S. Kahraman, D.F. De Jesus, A. El Ouaamari, G. Basile, R. Baker, and B. Yigit, et al. 2019. "Increased ß-cell proliferation before immune cell invasion prevents progression of type 1 diabetes." Nature Metabolism 1, no. 5:509-518. PNNL-SA-141695. doi:10.1038/s42255-019-0061-8
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
Nakayasu E.S., W. Qian, C. Evans-Molina, R. Mirmira, D.L. Eizirik, and T.O. Metz. 2019. "The role of proteomics in assessing beta-cell dysfunction and death in type 1 diabetes." Expert Review of Proteomics 16, no. 7:569-582. PNNL-SA-142336. doi:10.1080/14789450.2019.1634548
Sims E.K., H.T. Bahnson, J. Nyalwidhe, L. Haataja, A.K. Davis, C. Speake, and L.A. DiMeglio, et al. 2019. "Proinsulin Secretion Is a Persistent Feature of Type 1 Diabetes." Diabetes Care 42, no. 2:258-264. PNNL-SA-140217. doi:10.2337/dc17-2625
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
Zhao Y., C. Shanshuang, A.C. Swensen, W. Qian, and E. Gouaux. 2019. "Architecture and subunit arrangement of native AMPA receptors elucidated by cryo-EM." Science 364, no. 6438:355-362. PNNL-SA-141540. doi:10.1126/science.aaw8250

2018

Gupta M., D.F. De Jesus, S. Kahraman, I. Valdez, F. Shamsi, L. Yi, and A.C. Swensen, et al. 2018. "Insulin Receptor-Mediated Signaling Regulates Pluripotency Markers and Lineage Differentiation." Molecular Metabolism 18. PNNL-SA-136923. doi:10.1016/j.molmet.2018.09.003
Kramer P.A., J. Duan, M.J. Gaffrey, A.K. Shukla, L.L. Wang, T. Bammler, and W. Qian, et al. 2018. "Fatiguing Contractions Increase Protein S-Glutathionylation Occupancy in Mouse Skeletal Muscle." Redox Biology 17. PNNL-SA-135523. doi:10.1016/j.redox.2018.05.011
Yi L., A.C. Swensen, and W. Qian. 2018. "Serum biomarkers for diagnosis and prediction of type 1 diabetes." Translational Research 201. PNNL-SA-134879. doi:10.1016/j.trsl.2018.07.009
Zhang T., M.J. Gaffrey, B.D. Thrall, and W. Qian. 2018. "Mass spectrometry-based proteomics for system-level characterization of biological responses to engineered nanomaterials." Analytical and Bioanalytical Chemistry 410, no. 24:6067-6077. PNNL-SA-133275. doi:10.1007/s00216-018-1168-6
Zhu D., H. Si, P. Zhang, A. Geng, W. Zhang, B. Yang, and W. Qian, et al. 2018. "Genomics and biochemistry investigation on the metabolic pathway of milled wood and alkali lignin-derived aromatic metabolites of Comamonas serinivorans SP-35." Biotechnology for Biofuels 11. PNNL-SA-140577. doi:10.1186/s13068-018-1341-3
Zhu Y., P.D. Piehowski, R. Zhao, J. Chen, Y. Shen, R.J. Moore, and A.K. Shukla, et al. 2018. "Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells." Nature Communications 9, no. 1:882. PNNL-SA-125235. doi:10.1038/s41467-018-03367-w
Zhu Y., P.D. Piehowski, R.T. Kelly, and W. Qian. 2018. "Nanoproteomics Comes of Age." Expert Review of Proteomics 15, no. 11:865-871. PNNL-SA-136396. doi:10.1080/14789450.2018.1537787

2017

Duan J., M.J. Gaffrey, and W. Qian. 2017. "Quantitative Proteomic Characterization of Redox-dependent Post-translational Modifications on Protein Cysteines." Molecular Biosystems 13, no. 5:816-829. PNNL-SA-122934. doi:10.1039/c6mb00861e
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, no. 20:11848-11857. PNNL-SA-127385. doi:10.1021/acs.est.7b03158
Li M., Y. Gao, W. Qian, L. Shi, Y. Liu, W.C. Nelson, and C.D. Nicora, et al. 2017. "Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes." Environmental Microbiology Reports 9, no. 5:512-521. PNNL-SA-120732. doi:10.1111/1758-2229.12558
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 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." The Journal of Pathology 243, no. 1:78-88. PNNL-SA-119241. doi:10.1002/path.4929
Yang L., T. Stewart, M. Shi, G. Pottiez, R. Dator, R. Wu, and P. Aro, et al. 2017. "An alpha-synuclein MRM assay with diagnostic potential for Parkinson’s disease and monitoring disease progression." Proteomics - Clinical Applications 11, no. 7-8:Article No. 1700045. PNNL-SA-124743. doi:10.1002/prca.201700045
Zhu D., P. Zhang, C. Xie, W. Zhang, J. Sun, W. Qian, and B. Yang. 2017. "Biodegradation of Alkaline Lignin by Bacillus ligniniphilus L1." Biotechnology for Biofuels 10. PNNL-SA-124233. doi:10.1186/s13068-017-0735-y

2016

Ahmad R., C.D. Nicora, A.K. Shukla, R.D. Smith, W. Qian, and A.Y. Liu. 2016. "An efficient method for native protein purification in the selected range from prostate cancer tissue digests." Chinese Clinical Oncology 5, no. 6:78. PNNL-SA-123158. doi:10.21037/cco.2016.12.03
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
Chan C., M.A. Gritsenko, R.D. Smith, and W. Qian. 2016. "The Current State-of-the-Art of Quantitative Phosphoproteomics and Its Applications to Diabetes Research." Expert Review of Proteomics 13, no. 4:421-433. PNNL-SA-115406. doi:10.1586/14789450.2016.1164604
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
Huang E.L., P.D. Piehowski, D.J. Orton, R.J. Moore, W. Qian, C.P. Casey, and X. Sun, et al. 2016. "SNaPP: Simplified Nano-Proteomics Platform for reproducible global proteomic analysis of nanogram protein quantities." Endocrinology 157, no. 3:1307-14. PNNL-SA-111854. doi:10.1210/en.2015-1821
Park C., B.A. Johnson, J. Duan, J. Park, J.J. Day, D.R. Gang, and W. Qian, et al. 2016. "9-Fluoenylmethyl (Fm) Disulfides: Biomimetic Precursors for Persulfides." Organic Letters 18, no. 5:904-907. PNNL-SA-115055. doi:10.1021/acs.orglett.5b03557
Quaamari A., E. Dirice, N. Gedeon, J. Hu, J. Zhou, J. Shirakawa, and L. Hou, et al. 2016. "SerpinB1 Promotes Pancreatic ß Cell Proliferation." Cell Metabolism 23, no. 1:194-205. PNNL-SA-114412. doi:10.1016/j.cmet.2015.12.001
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 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

2015

Bhatt S., M. Gupta, M. Khamaisi, R. Martinez, M.A. Gritsenko, B. Wagner, and P. Guye, et al. 2015. "Preserved DNA Damage Checkpoint Pathway Protects against Complications in Long-Standing Type 1 Diabetes." Cell Metabolism 22, no. 2:239-252. PNNL-SA-113658. doi:10.1016/j.cmet.2015.07.015
Duan J., V.K. Kodali, M.J. Gaffrey, J. Guo, R.K. Chu, D.G. Camp, and R.D. Smith, et al. 2015. "Quantitative Profiling of Protein S-Glutathionylation Reveals Redox-Dependent Regulation of Macrophage Function During Nanoparticle-Induced Oxidative Stress." ACS Nano 10, no. 1:524-538. PNNL-SA-112721. doi:10.1021/acsnano.5b05524
EL Ouaaman A., J. Zhou, C. Liew, J. Shirakawa, E. Dirice, N. Gedeon, and S. Kahraman, et al. 2015. "Compensatory Islet Response to Insulin Resistance Revealed by Quantitative Proteomics." Journal of Proteome Research 14, no. 8:3111-3122. PNNL-SA-100672. doi:10.1021/acs.jproteome.5b00587
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
Kramer P.A., J. Duan, W. Qian, and D.J. Marcinek. 2015. "The measurement of reversible redox dependent post-translational modifications and their regulation of mitochondrial and skeletal muscle function." Frontiers in Physiology 6. PNNL-SA-114339. doi:10.3389/fphys.2015.00347
Sigdel T.K., Y. NG, S. Lee, C.D. Nicora, W. Qian, R.D. Smith, and D.G. Camp, et al. 2015. "Perturbations in the Urinary Exosome in Transplant Rejection." Frontiers of Medicine 1. PNNL-SA-106428. doi:10.3389/fmed.2014.00057

2014

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
Nakayasu E.S., S. Wu, M.A. Sydor, A.K. Shukla, K.K. Weitz, R.J. Moore, and K.K. Hixson, et al. 2014. "A Method to determine lysine acetylation stoichiometries." International Journal of Proteomics 2014. PNNL-SA-96571. doi:10.1155/2014/730725
Ryu S., W. Qian, D.G. Camp, R.D. Smith, R.G. Tompkins, R.W. Davis, and W. Xiao. 2014. "Detecting differential protein expression in large-scale population proteomics." Bioinformatics 30, no. 19:2741-2746. PNNL-SA-100193. doi:10.1093/bioinformatics/btu341
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
Shin A.C., M. Fasshauer, N. Filatova, L.A. Grundell, E. Zielinski, J. Zhou, and T. Scherer, et al. 2014. "Brain insulin lowers circulating BCAA levels by inducing hepatic BCAA catabolism." Cell Metabolism 20, no. 5:898-909. PNNL-SA-103823. doi:10.1016/j.cmet.2014.09.003
Sigdel T.K., C.D. Nicora, S. Hsieh, H. Dai, W. Qian, D.G. Camp, and M.M. Sarwal. 2014. "Optimization for Peptide Sample Preparation for Urine Peptidomics." Clinical Proteomics 11. PNNL-SA-98818. doi:10.1186/1559-0275-11-7
Sigdel T.K., N. Salomonis, C.D. Nicora, S. Ryu, J. He, V. Dinh, and D.J. Orton, et al. 2014. "The Identification of Novel Potential Injury Mechanisms and Candidate Biomarkers in Renal Allograft Rejection by Quantitative Proteomics." Molecular & Cellular Proteomics. MCP 13, no. 2:621-631. PNWD-SA-10124. doi:10.1074/mcp.M113.030577
Su D., M.J. Gaffrey, J. Guo, K.E. Hatchell, R.K. Chu, T.R. Clauss, and J.T. Aldrich, et al. 2014. "Proteomic Identification and Quantification of S-glutathionylation in Mouse Macrophages Using Resin-Assisted Enrichment and Isobaric Labeling." Free Radical Biology & Medicine 67. PNNL-SA-96702. doi:10.1016/j.freeradbiomed.2013.12.004
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
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
Zhang Q., M.M. Matzke, A.A. Schepmoes, R.J. Moore, B.M. Webb-Robertson, Z. Hu, and M.E. Monroe, et al. 2014. "High and Low Doses of Ionizing Radiation Induce Different Secretome Profiles in a Human Skin Model." PLoS One 9, no. 3:Article No. e92332. PNNL-SA-98075. doi:10.1371/journal.pone.0092332

2013

Dai Z., U.K. Aryal, A.K. Shukla, W. Qian, R.D. Smith, J.K. Magnuson, and W.S. Adney, et al. 2013. "Impact of alg3 gene deletion on growth, development, pigment production, protein secretion, and functions of recombinant Trichoderma reesei cellobiohydrolases in Aspergillus niger." Fungal Genetics and Biology : FG & B 61. PNNL-SA-93855. doi:10.1016/j.fgb.2013.09.004
El Ouaamari A., D. Kawamori, E. Dirice, C. Liew, J.L. Shadrach, J. Hu, and H. Katsuta, et al. 2013. "Liver-derived systemic factors drive ß-cell hyperplasia in insulin resistant states." Cell Reports 3, no. 2:401-410. PNNL-SA-93433. doi:10.1016/j.celrep.2013.01.007
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
Fu N., D. Su, J.R. Cort, B. Chen, Y. Xiong, W. Qian, and A. Konopka, et al. 2013. "Synthesis and Application of an Environmentally Insensitive Cy3-Based Arsenical Fluorescent Probe to Identify Adaptive Microbial Responses Involving Proximal Dithiol Oxidation." Journal of the American Chemical Society 135, no. 9:3567-3575. PNNL-SA-92302. doi:10.1021/ja3117284
Kim J., M.E. Monroe, D.G. Camp, R.D. Smith, and W. Qian. 2013. "In-Source Fragmentation and the Sources of Partially Tryptic Peptides in Shotgun Proteomics." Journal of Proteome Research 12, no. 2:910-916. PNNL-SA-91081. doi:10.1021/pr300955f
Kim J., Z. Dai, U.K. Aryal, R.J. Moore, D.G. Camp, S.E. Baker, and R.D. Smith, et al. 2013. "Resin-assisted Enrichment of N-terminal Peptides for Characterizing Proteolytic Processing." Analytical Chemistry 85, no. 14:6826-6832. PNNL-SA-92785. doi:10.1021/ac401000q
Nakayasu E.S., C. Ansong, J.N. Brown, F. Yang, D. Lopez-Ferrer, W. Qian, and R.D. Smith, et al. 2013. "Evaluation of selected binding domains for the analysis of ubiquitinated proteomes." Journal of the American Society for Mass Spectrometry 24, no. 8:1214-1223. PNNL-SA-83169. doi:10.1007/s13361-013-0619-8
Seok J., H.S. Warren, A.G. Cuenca, M. Mindrinos, H.V. Baker, W. Xu, and D.R. Richards, et al. 2013. "Analysis of factorial time-course microarrays." Proceedings of the National Academy of Sciences of the United States of America 110, no. 9:3507-3512. PNWD-SA-10475. doi:10.1073/pnas.1222878110
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
Su D., A.K. Shukla, B. Chen, J. Kim, E.S. Nakayasu, Y. Qu, and U.K. Aryal, et al. 2013. "Quantitative Site-specific Reactivity Profiling of S-Nitrosylation in Mouse Skeletal Muscle Using Cysteinyl Peptide Enrichment Coupled with Mass Spectrometry." Free Radical Biology & Medicine 57. PNNL-SA-89035. doi:10.1016/j.freeradbiomed.2012.12.010
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

2012

Aryal U.K., C.T. Lin, J. Kim, T.H. Heibeck, J. Wang, W. Qian, and Y. Lin. 2012. "Identification of phosphorylated butyrylcholinesterase in human plasma using immunoaffinity purification and mass spectrometry." Analytica Chimica Acta 723. PNNL-SA-83170.
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 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
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
Qian W., B.O. Petritis, C.D. Nicora, and R.D. Smith. 2011. "Trypsin-catalyzed oxygen-18 labeling for quantitative proteomics." In Gel-Free Proteomics, Methods and Protocols: Methods in Molecular Biology, edited by K Gevaert and J Vandekerckhove. 43-54. Totowa, New Jersey:Humana Press Inc. PNNL-SA-78931.
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., F. Yang, W. Qian, R.N. Brown, Y. Wang, E.D. Merkley, and J.H. Park, et al. 2011. "Identification of c-Type Heme-Containing Peptides Using Non-Activated Immobilized Metal Affinity Cchromatography Resin Enrichment and Higher-Energy Collisional Dissociation." Analytical Chemistry 83, no. 19:7260-7268. PNNL-SA-77198. doi:10.1021/ac2000829
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
Zhou J., G.P. Dann, C.W. Liew, R.D. Smith, R.N. Kulkarni, and W. Qian. 2011. "Unraveling pancreatic islet biology by quantitative proteomics." Expert Review of Proteomics 8, no. 4:495-504. PNNL-SA-77799. doi:10.1586/epr.11.39

2010

Kotz K.T., W. Xiao, C. Miller-Graziano, W. Qian, A. Russom, E.A. Warner, and L.L. Moldawer, et al. 2010. "Clinical Microfluidics for Neutrophil Genomics and Proteomics." Nature Medicine 16, no. 9:1042-1048. PNWD-SA-8973. doi:10.1038/nm.2205
Petyuk V.A., W. Qian, R.D. Smith, and D.J. Smith. 2010. "Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry." Methods 50, no. 2:77-84. PNNL-SA-68829.
Qian W., B.O. Petritis, A. Kaushal, C.C. Finnerty, M.G. Jescheke, M.E. Monroe, and R.J. Moore, et al. 2010. "Plasma Proteome Response to Severe Burn Injury Revealed by 18O-Labeled “Universal” Reference-based Quantitative Proteomics." Journal of Proteome Research 9, no. 9:4779-4789. PNWD-SA-9014.
Sigdel T.K., A. Kaushal, M.A. Gritsenko, A.D. Norbeck, W. Qian, W. Xiao, and D.G. Camp, et al. 2010. "Shotgun Proteomics Identifies Proteins Specific for Acute Renal Transplant Rejection." Proteomics - Clinical Applications 4, no. 1:32-47. PNNL-SA-68069. doi:10.1002/prca.200900124
Tang Z., H. Wu, D. Du, J. Wang, H. Wang, W. Qian, and D.J. Bigelow, et al. 2010. "Sensitive Immunoassays of Nitrated Fibrinogen in Human Biofluids." Talanta 81, no. 4-5:1662-1669. PNNL-SA-71863.
True L.D., H. Zhang, M. Ye, C. Huang, P.S. Nelson, P.D. Von Haller, and L.W. Tjoelker, et al. 2010. "CD90/THY1 is over-expressed in prostate cancer-associated fibroblasts and could serve as a cancer biomarker." Modern Pathology 23, no. 10:1346-1356. PNNL-SA-74146.
Zhang H., R.N. Brown, W. Qian, M.E. Monroe, S.O. Purvine, R.J. Moore, and M.A. Gritsenko, et al. 2010. "Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling." Journal of Proteome Research 9, no. 5:2160-2169. PNNL-SA-67314.
Zhang X., J. Zhou, M.H. Chin, A.A. Schepmoes, V.A. Petyuk, K.K. Weitz, and B.O. Petritis, et al. 2010. "Region-Specific Protein Abundance Changes in the Brain of MPTP-induced Parkinson’s Disease Mouse Model." Journal of Proteome Research 9, no. 3:1496-1509. PNNL-SA-67444. doi:10.1021/pr901024z
Zhang X., M.E. Monroe, B. Chen, M.H. Chin, T.H. Heibeck, A.A. Schepmoes, and F. Yang, et al. 2010. "Endogenous 3, 4- Dihydroxyphenylalanine and Dopaquinone Modifications on Protein Tyrosine: links to mitochondrially derived oxidative stress via hydroxyl radical." Molecular & Cellular Proteomics. MCP 9, no. 6:1199-1208. PNNL-SA-65899.
Zhou J., A.A. Schepmoes, X. Zhang, R.J. Moore, M.E. Monroe, J. Lee, and D.G. Camp, et al. 2010. "Improved LC-MS/MS Spectral Counting Statistics by Recovering Low Scoring Spectra Matched to Confidently Identified Peptide Sequences." Journal of Proteome Research 9, no. 11:5698-5704. PNNL-SA-74147. doi:10.1021/pr100508p

2009

Heibeck T.H., S. Ding, L.K. Opresko, R. Zhao, A.A. Schepmoes, F. Yang, and A.V. Tolmachev, et al. 2009. "An Extensive Survey of Tyrosine Phosphorylation Revealing New Sites in Human Mammary Epithelial Cells." Journal of Proteome Research 8, no. 8:3852-3861. PNNL-SA-63993.
Karpievitch Y., J.R. Stanley, T. Taverner, J. Huang, J.N. Adkins, C. Ansong, and F. Heffron, et al. 2009. "A statistical framework for protein quantitation in bottom-up MS-based proteomics." Bioinformatics 25, no. 16:2028-2034. PNNL-SA-66740. doi:10.1093/bioinformatics/btp362
Karpievitch Y., J.R. Stanley, T. Taverner, J. Huang, J.N. Adkins, C. Ansong, and F. Heffron, et al. 2009. "A Statistical Framework for Protein Quantitation in Bottom-Up MS-Based Proteomics." Bioinformatics 25, no. 16:2028-2034. PNNL-SA-70100.
Park C.C., V.A. Petyuk, W. Qian, R.D. Smith, and D.J. Smith. 2009. "Dual spatial maps of transcript and protein abundance in the mouse brain." Expert Review of Proteomics 6, no. 3:243-249. PNWD-SA-8709.
Petritis B.O., W. Qian, D.G. Camp, and R.D. Smith. 2009. "A Simple Procedure for Effective Quenching of Trypsin Activity and Prevention of 18O-Labeling Back-Exchange." Journal of Proteome Research 8, no. 5:2157-2163. PNWD-SA-8385. doi:10.1021/pr800971w
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.
Schepmoes A.A., Q. Zhang, B.O. Petritis, W. Qian, and R.D. Smith. 2009. "N-Terminal Enrichment: Developing a Protocol to Detect Specific Proteolytic Fragments." Journal of Biomolecular Techniques:JBT 20, no. 5:263-265. PNNL-SA-75602.
Zhou J., B.O. Petritis, K. Petritis, A.D. Norbeck, K.K. Weitz, R.J. Moore, and D.G. Camp, et al. 2009. "Mouse-Specific Tandem IgY7-SuperMix Immunoaffinity Separations for Improved LC-MS/MS Coverage of the Plasma Proteome." Journal of Proteome Research 8, no. 11:5387-5395. PNNL-SA-67312.

2008

Bigelow D.J., and W. Qian. 2008. "Quantitative Proteome Mapping of Nitrotyrosines." In Methods in Enzymology, Nitric Oxide Part F: Oxidative and Nitrosative Stress in Redox Regulation of Cell Signaling. 191-205. Amsterdam:Elsevier. PNNL-SA-56770.
Chin M.H., W. Qian, H. Wang, V.A. Petyuk, J.S. Bloom, D.M. Sforza, and G. Lacan, et al. 2008. "Mitochondrial dysfunction, oxidative stress and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson’s disease." Journal of Proteome Research 7, no. 2:666-677. PNNL-SA-58152. doi:10.1021/pr070546l
Ding S., Y. Wang, J.M. Jacobs, W. Qian, F. Yang, A.V. Tolmachev, and X. Du, et al. 2008. "Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step ¹8O Labeling Coupled with Immobilized Metal-ion Affinity Chromatography." Journal of Proteome Research 7, no. 10:4215-24. PNNL-SA-52241. doi:10.1021/pr7007785
Kelly R.T., J.S. Page, R. Zhao, W. Qian, H.M. Mottaz, K. Tang, and R.D. Smith. 2008. "Capillary-Based Multi Nanoelectrospray Emitters: Improvements in Ion Transmission Efficiency and Implementation with Capillary Reversed-Phase LC-ESI-MS." Analytical Chemistry 80, no. 1:143-149. PNNL-SA-56420. doi:10.1021/ac701647s
Lopez-Ferrer D., T.H. Heibeck, K. Petritis, K.K. Hixson, W. Qian, M.E. Monroe, and A.M. Mayampurath, et al. 2008. "Rapid Sample Processing For LC-MS Based Quantitative Proteomics Using High Intensity Focused Ultrasounds." Journal of Proteome Research 7, no. 9:3860-3867. PNNL-SA-59400. doi:10.1021/pr800161x
Metz T.O., W. Qian, J.M. Jacobs, M.A. Gritsenko, R.J. Moore, A.D. Polpitiya, and M.E. Monroe, et al. 2008. "Application of proteomics in the discovery of candidate protein biomarkers in a Diabetes Autoantibody Standardization Program sample subset." Journal of Proteome Research 7, no. 2:698-707. PNNL-SA-56533. doi:10.1021/pr700606w
Pasa-Tolic L., J.M. Jacobs, W. Qian, and R.D. Smith. 2008. "Quantitative Proteomics using Nano-LC with High Accuracy Mass Spectrometry." In Clinical Proteomics: From Diagnosis to Therapy, edited by JE Van Eyk and MJ Dunn. 89-100. Weinheim:Wiley-VCH. PNNL-SA-51867.
Petyuk V.A., N. Jaitly, R.J. Moore, J. Ding, T.O. Metz, K. Tang, and M.E. Monroe, et al. 2008. "Elimination of Systematic Mass Measurement Errors in Liquid Chromatography-Mass Spectrometry Based Proteomics using Regression Models and a priori Partial Knowledge of the Sample Content." Analytical Chemistry 80, no. 3:693-706. PNNL-SA-56693. doi:10.1021/ac701863d
Petyuk V.A., W. Qian, C. Hinault, M.A. Gritsenko, M. Singhal, M.E. Monroe, and D.G. Camp, et al. 2008. "Characterization of the mouse pancreatic islet proteome and comparative analysis with other mouse tissues." Journal of Proteome Research 7, no. 8:3114-3126. PNNL-SA-58155. doi:10.1021/pr800205b
Polpitiya A.D., W. Qian, N. Jaitly, V.A. Petyuk, J.N. Adkins, D.G. Camp, and G.A. Anderson, et al. 2008. "DAnTE: a statistical tool for quantitative analysis of -omics data." Bioinformatics 24, no. 13:1556-1558. PNNL-SA-58107. doi:10.1093/bioinformatics/btn217
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
Shen Y., N. Tolic, K.K. Hixson, S.O. Purvine, L. Pasa-Tolic, W. Qian, and J.N. Adkins, et al. 2008. "Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags." Analytical Chemistry 80, no. 6:1871-82. PNNL-SA-56012. doi:10.1021/ac702328x

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.
Chin M.H., A.B. Geng, A.H. Khan, W. Qian, V.A. Petyuk, J. Boline, and S. Levy, et al. 2007. "A genome-scale map of expression for a mouse brain section obtained using voxelation." Physiological Genomics 30, no. 3:313-321. PNWD-SA-7823.
Ding S., W. Qian, and R.D. Smith. 2007. "Quantitative Proteomic Approaches for Studying Phosphotyrosine Signaling." Expert Review of Proteomics 4, no. 1:13-23. PNWD-SA-7569. doi:doi:10.1586/14789450.4.1.13
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.
Petyuk V.A., W. Qian, M.H. Chin, H.H. Wang, E.A. Livesay, M.E. Monroe, and J.N. Adkins, et al. 2007. "Spatial Mapping of Protein Abundances in the Mouse Brain by Voxelation Integrated with High-Throughput Liquid Chromatography - Mass Spectrometry." Genome Research 17, no. 3:328-336. PNNL-SA-49342. doi:10.1101/gr.5799207
Wang Y., S. Ding, W. Wang, J.M. Jacobs, W. Qian, R.J. Moore, and F. Yang, et al. 2007. "Profiling Signaling Polarity in Chemotactic Cells." Proceedings of the National Academy of Sciences of the United States of America 104, no. 20:8328-8333. PNNL-SA-51866. doi:10.1073/pnas.0701103104
Zhang Q., W. Qian, T.V. Knyushko, T.R. Clauss, S.O. Purvine, R.J. Moore, and C.A. Sacksteder, et al. 2007. "A Method for Selective Enrichment and Analysis of Nitrotyrosine-Containing Peptides in Complex Proteome Samples." Journal of Proteome Research 6, no. 6:2257-2268. PNNL-SA-53248. doi:10.1021/pr0606934

2006

Callister S.J., R.C. Barry, J.N. Adkins, E.T. Johnson, W. Qian, B.M. Webb-Robertson, and R.D. Smith, et al. 2006. "Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics." Journal of Proteome Research 5, no. 2:277-286. PNNL-SA-46453. doi:10.1021/pr050300l
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
Metz T.O., J.M. Jacobs, M.A. Gritsenko, G. Fontes, W. Qian, D.G. Camp, and V.J. Poitout, et al. 2006. "Characterization of the Human Pancreatic Islet Proteome by Two-Dimensional LC/MS/MS." Journal of Proteome Research 5, no. 12:3345-3354. PNNL-SA-49730. doi:10.1021/pr060322n
Petritis K., L.J. Kangas, B. Yan, M.E. Monroe, E.F. Strittmatter, W. Qian, and J.N. Adkins, et al. 2006. "Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information." Analytical Chemistry 78, no. 14:5026-5039. PNNL-SA-50263. doi:10.1021/ac060143p
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
Sacksteder C.A., W. Qian, T.V. Knyushko, H.H. Wang, M.H. Chin, G. Lacan, and W.P. Melega, et al. 2006. "Endogenously Nitrated Proteins in Mouse Brain: Links To Neurodegenerative Disease." Biochemistry 45, no. 26:8009-8022. PNNL-SA-47471. doi:10.1021/bi060474w
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.
Zimmer J.S., M.E. Monroe, W. Qian, and R.D. Smith. 2006. "Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach." Mass Spectrometry Reviews 25, no. 3:450-482. PNNL-SA-43136.

2005

Jacobs J.M., D.L. Diamond, E.Y. Chan, M.A. Gritsenko, W. Qian, M. Stastna, and T. Baas, et al. 2005. "Proteome Analysis of Liver Cells Expressing a Full- Length Hepatitis C Virus (HCV) Replicon and Biopsy Specimens of Posttransplantation Liver from HCV-Infected Patients." Journal of Virology 79, no. 12:7558-7569. PNWD-SA-6678.
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
Jacobs J.M., M.E. Monroe, W. Qian, Y. Shen, G.A. Anderson, and R.D. Smith. 2005. "Ultra-Sensitive, High Throughput and Quantitative Proteomics Measurements." International Journal of Mass Spectrometry 240, no. 3:195-212. PNNL-SA-42919.
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.
Masselon C.D., L. Pasa-Tolic, N. Tolic, G.A. Anderson, B. Bogdanov, A.N. Vilkov, and Y. Shen, et al. 2005. "Targeted Comparative Proteomics by Liquid Chromatography - Tandem Fourier ion cyclotron resonance Mass Spectrometry." Analytical Chemistry 77, no. 2:400-406. PNNL-SA-42470.
Qian W., J.M. Jacobs, D.G. Camp, M.E. Monroe, R.J. Moore, M.A. Gritsenko, and S.E. Calvano, et al. 2005. "Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry." Proteomics 5, no. 2:572-584. PNNL-SA-40692. doi:10.1002/pmic.200400942
Qian W., J.M. Jacobs, D.G. Camp, M.E. Monroe, R.J. Moore, M.A. Gritsenko, and S.E. Calvano, et al. 2005. "Comparative Proteome Analyses of Human Plasma Following in vivo Lipopolysaccharide Administration Using Multidimensional Separations Coupled with Tandem Mass Spectrometry." Proteomics 5, no. 2:572-584. PNNL-SA-41257.
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.
Wang H.H., W. Qian, H.M. Mottaz, T.R. Clauss, D.J. Anderson, R.J. Moore, and D.G. Camp, et al. 2005. "Development and Evaluation of a Micro- and Nanoscale Proteomic Sample Preparation Method." Journal of Proteome Research 4, no. 6:2397-2403. PNNL-SA-45347. doi:10.1021/pr050160f

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.
Qian W., D.G. Camp, and R.D. Smith. 2004. "High Throughput Proteomics Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Expert Review of Proteomics 1, no. 1:87-95. PNNL-SA-41680.

2003

Qian W., M.B. Goshe, D.G. Camp, L. Yu, K. Tang, and R.D. Smith. 2003. "Phosphoprotein Isotope-Coded Solid-Phase Tag Approach for Enrichment and Quantitative Analysis of Phosphopeptides from Complex Mixtures." Analytical Chemistry 75, no. 20:5441-5450. PNNL-SA-38312