Staff information

PNNL Publications

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
• Day N.J., S.S. Kelly, L. Liu, T.A. Mansfield, M.J. Gaffrey, J.B. Trejo, and T.J. Sagendorf, et al. 2024. "Signatures of Cysteine Oxidation on Muscle Structural and Contractile Proteins Are Associated with Physical Performance and Muscle Function in Older Adults: Study of Muscle, Mobility and Aging (SOMMA)." Aging Cell. PNNL-SA-192090. doi:10.1111/acel.14094
• De Jesus D.F., Z. Zhang, N.K. Brown, X. Li, L. Xiao, J. Hu, and M.J. Gaffrey, et al. 2024. "Redox Regulation of m6A Methyltransferase METTL3 in Human ß-cells Controls the Innate Immune Response in Type 1 Diabetes." Nature Cell Biology 26, no. 3:421 - 437. PNNL-SA-192085. doi:10.1038/s41556-024-01368-0
• Fu J., B. McKinley, B. James, W.B. Chrisler, L. Markillie, M.J. Gaffrey, and H.D. Mitchell, et al. 2024. "Cell-type-specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems." The Plant Journal 118, no. 5:1668-1688. PNNL-SA-201514. doi:10.1111/tpj.16690
• 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

2023

• Day N.J., T. Zhang, M.J. Gaffrey, B.D. Thrall, and W. Qian. 2023. "Assessment of the Biological Impact of Engineered Nanomaterials Using Mass Spectrometry-based MultiOmics Approaches." In Impact of Engineered Nanomaterials in Genomics and Epigenomics, edited by S.C. Sahu. 331 - 354. Hoboken, New Jersey:John Wiley & Sons. PNNL-SA-177428. doi:10.1002/9781119896258.ch15

2022

• Anderson C.E., J. Zhang, L. Markillie, H.D. Mitchell, W.B. Chrisler, M.J. Gaffrey, and G. Orr, et al. 2022. "Capturing an Early Gene Induction Event during Wood Decay by the Brown Rot Fungus Rhodonia placenta." Applied and Environmental Microbiology 88, no. 8:Art. No. e00188-22. PNNL-SA-172027. doi:10.1128/aem.00188-22
• Day N.J., T. Zhang, M.J. Gaffrey, R. Zhao, T.L. Fillmore, R.J. Moore, and G. Rodney, et al. 2022. "A Deep Redox Proteome Profiling Workflow and Its Application to Skeletal Muscle of a Duchenne Muscular Dystrophy Model." Free Radical Biology & Medicine 193, no. Part 1:373-384. PNNL-SA-156410. doi:10.1016/j.freeradbiomed.2022.10.300
• Li X., T. Zhang, N.J. Day, S. Feng, M.J. Gaffrey, and W. Qian. 2022. "Defining the S-glutathionylation Proteome by Biochemical and Mass Spectrometric Approaches." Antioxidants 11, no. 11:Art. No. 2272. PNNL-SA-179617. doi:10.3390/antiox11112272
• Zhang J., L. Markillie, H.D. Mitchell, M.J. Gaffrey, G. Orr, and J.S. Schilling. 2022. "Distinctive carbon repression effects in the carbohydrate-selective wood decay fungus Rhodonia placenta." Fungal Genetics and Biology : FG & B 159. PNNL-SA-170453. doi:10.1016/j.fgb.2022.103673
• Zhang T., N.J. Day, M.J. Gaffrey, K.K. Weitz, I.K. Attah, P. Mimche, and R. Paine III, et al. 2022. "Regulation of hyperoxia-induced neonatal lung injury via post-translational cysteine redox modifications." Redox Biology 55. PNNL-SA-176815. doi:10.1016/j.redox.2022.102405

2021

• 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
• 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
• 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
• 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
• 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

2020

• 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
• 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
• 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
• 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
• Tan Z., J. Zhu, P.M. Stemmer, L. Sun, Z. Yang, K.D. Martin, and M.J. Gaffrey, et al. 2020. "Comprehensive Detection of Single Amino Acid Variants and Evaluation of Their Deleterious Potential in a PANC-1 Cell Line." Journal of Proteome Research 19, no. 4:1635-1646. PNNL-SA-153237. doi:10.1021/acs.jproteome.9b00840
• 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
• 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
• 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
• 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
• 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

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
• Dai Y., H.A. Ogilvie, Y. Liu, M. Huang, L. Markillie, H.D. Mitchell, and E.J. Borrego, et al. 2019. "Rosette core fungal resistance in Arabidopsis thaliana." Planta 250, no. 6:1941-1953. PNNL-SA-147546. doi:10.1007/s00425-019-03273-5
• Dai Y., H.A. Ogilvie, Y. Liu, M. Huang, L. Markillie, H.D. Mitchell, and E.J. Borrego, et al. 2019. "Rosette Core Fungal Resistance in Arabidopsis thaliana." Planta. PNNL-SA-142134. doi:10.1007/s00425-019-03273-5
• Li X., Y. He, L. Zhang, Z. Xu, H. Ben, M.J. Gaffrey, and Y. Yang, et al. 2019. "Discovery of Potential Pathways for Biological Conversion of Poplar Wood to Lipids by Co-Fermentation of Rhodococci Strains." Biotechnology for Biofuels 12. PNNL-SA-136201. doi:10.1186/s13068-019-1395-x
• 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

• Cui Y., D. Hu, L. Markillie, W.B. Chrisler, M.J. Gaffrey, C.K. Ansong, and L. Sussel, et al. 2018. "Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells." Nucleic Acids Research 46, no. 2:Article No. e7. PNNL-SA-126413. doi:10.1093/nar/gkx874
• 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
• 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
• Smith J.N., D.G. Thomas, H.D. Jolley, V.K. Kodali, M.H. Littke, P. Munusamy, and D.R. Baer, et al. 2018. "All that is Silver is not Toxic: Silver Ion and Particle Kinetics Reveals the Role of Silver Ion Aging and Dosimetry on the Toxicity of Silver Nanoparticles." Particle and Fibre Toxicology 15. PNNL-SA-135829. doi:10.1186/s12989-018-0283-z
• 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

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
• Orellana R., G. Chaput, L. Markillie, H.D. Mitchell, M.J. Gaffrey, G. Orr, and K.M. Deangelis. 2017. "Multi-time series RNA-seq analysis of Enterobacter lignolyticusSCF1 during growth in lignin-amended medium." PLoS One 12, no. 10:e0186440. PNNL-SA-131719. doi:10.1371/journal.pone.0186440

2016

• Mitchell H.D., L. Markillie, W.B. Chrisler, M.J. Gaffrey, D. Hu, C.J. Szymanski, and Y. Xie, et al. 2016. "Cells Respond to Distinct Nanoparticle Properties with Multiple Strategies as Revealed by Single-Cell RNA-Seq." ACS Nano 10, no. 11:10173-10185. PNNL-SA-121323. doi:10.1021/acsnano.6b05452

2015

• 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

2014

• Guo J., A.Y. Nguyen, Z. Dai, D. Su, M.J. Gaffrey, R.J. Moore, and J.M. Jacobs, et al. 2014. "Proteome-wide Light/Dark Modulation of Thiol Oxidation in Cyanobacteria Revealed by Quantitative Site-Specific Redox Proteomics." Molecular & Cellular Proteomics 13, no. 12:3270-3285. PNNL-SA-100244. doi:10.1074/mcp.M114.041160
• 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
• 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
• 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

2013

• Sharma G., V.K. Kodali, M.J. Gaffrey, W. Wang, K.R. Minard, N.J. Karin, and J.G. Teeguarden, et al. 2013. "Iron Oxide Nanoparticle Agglomeration Influences Dose-Rates and Modulates Oxidative Stress Mediated Dose-Response Profiles In Vitro." Nanotoxicology 8, no. 6:663-675. PNNL-SA-93447. doi:10.3109/17435390.2013.822115