Bioanalytical Chemist, Lab Fellow
Bioanalytical Chemist, Lab Fellow


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.


  • 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



  • 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


  • 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


  • 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


  • 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


  • 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


  • 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


  • 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


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  • 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


  • 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.


  • 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


  • 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.


  • 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