Collaborative research projects in the PNNL NIH P41 Biomedical Technology Research Center 'Proteomics research resource for integrative biology'
EMSL Project ID
50604
Abstract
Collaborative research projects in the PNNL NIH P41 Biomedical Technology Research Center 'Proteomics research resource for integrative biology'
Project Details
Start Date
2018-10-09
End Date
2021-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Block Design with Common Reference Samples Enables Robust Large-Scale Label-Free Quantitative Proteome Profiling
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
Meta-analysis of peptides to detect protein significance
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 Its Interface 13. PNNL-SA-152554. doi:10.4310/sii.2020.v13.n4.a4
National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions
Kagan J., R.L. Moritz, R. Mazurchuk, J. Lee, P. Kharchenko, O. Rozenblatt-Rosen, and E. Ruppin, et al. 2020. "NCI Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions." Journal of Proteome Research. PNNL-SA-152101. doi:10.1021/acs.jproteome.0c00021
Benzo[a]pyrene Induction of Glutathione S-Transferases: An Activity-Based Protein Profiling Investigation
Stoddard E.G., B.J. Killinger, S. Nag, J. Martin, R.A. Corley, J.N. Smith, and A.T. Wright. 2019. "Benzo[a]pyrene Induction of Glutathione S-Transferases: An Activity-Based Protein Profiling Investigation." Chemical Research in Toxicology 32, no. 6:1259-1267. PNNL-SA-137670. doi:10.1021/acs.chemrestox.9b00069
Evaluating the structural complexity of isomeric bile acids with ion mobility spectrometry
Zheng X., F.B. Smith, A. Noor, J. Cai, R.D. Smith, and E.S. Baker. 2019. "Evaluating the structural complexity of isomeric bile acids with ion mobility spectrometry." Analytical and Bioanalytical Chemistry. PNNL-SA-147447. doi:10.1007/s00216-019-01869-0
Effects of ingested nanocellulose on intestinal microbiota and homeostasis in Wistar Han rats
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." PLoS Biology. PNNL-SA-150324. doi:10.1016/j.impact.2020.100216.
An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics
Tsai C., R. Zhao, R.J. Moore, S.M. Williams, K.D. Schultz, L. Pasa Tolic, and K.D. Rodland, et al. 2020. "An improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) strategy for precise quantitative single-cell proteomics." Molecular and Cellular Proteomics. PNNL-SA-149183. doi:10.1074/mcp.RA119.001857
Accurate Identification of Deamidation and Citrullination from Global Shotgun Proteomics Data Using a Dual-Search Delta Score Strategy
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
Metabolite, Protein, and Lipid Extraction (MPLEx): A Method that Simultaneously Inactivates Middle East Respiratory Syndrome Coronavirus and Allows Analysis of Multiple Host Cell Components Following Infection
Nicora C.D., A. Sims, K.J. Bloodsworth, Y. Kim, R.J. Moore, J.E. Kyle, and E.S. Nakayasu, et al. 2020. "Metabolite, Protein, and Lipid Extraction (MPLEx): a method that simultaneously inactivates Middle East respiratory syndrome coronavirus and allows analysis of multiple host cell components following infection." In MERS Coronavirus: Methods and Protocols, edited by R. Vijay. 173-194. New York, New York:Humana. PNNL-SA-142077. doi:10.1007/978-1-0716-0211-9_14
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
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
A proteome-wide assessment of the oxidative stress paradigm for metal and metal-oxide nanomaterials in human macrophages
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
Stable Acinar Progenitor Cell Model Identifies Treacle-Dependent Radioresistance
Weber T.J., W. Qian, J.N. Smith, M.A. Gritsenko, D. Hu, W.B. Chrisler, and C. Timchalk. 2019. "Stable Acinar Progenitor Cell Model Identifies Treacle-Dependent Radioresistance." Radiation Research 192, no. 2:135-144. PNNL-SA-140501. doi:10.1667/RR15342.1
Tandem Mass Tag Labeling Facilitates Reversed-Phase Liquid Chromatography-Mass Spectrometry Analysis of Hydrophilic Phosphopeptides
Tsai C., J.S. Smith, K. Krajewski, R. Zhao, A.M. Moghieb, C.D. Nicora, and X. Xiong, et al. 2019. "TMT labeling facilitates RPLC-MS analysis of hydrophilic phosphopeptides." Analytical Chemistry. PNNL-SA-142808. doi:10.1021/acs.analchem.9b01814
Automated Nanoflow Two-Dimensional Reversed-Phase Liquid Chromatography System Enables In-Depth Proteome and Phosphoproteome Profiling of Nanoscale Samples
Dou M., C. Tsai, P.D. Piehowski, Y. Wang, T.L. Fillmore, R. Zhao, and R.J. Moore, et al. 2019. "Automated Nanoflow Two-Dimensional Reversed-Phase Liquid Chromatography System Enables In-Depth Proteome and Phosphoproteome Profiling of Nanoscale Samples." Analytical Chemistry 91, no. 15:9707-9715. PNNL-SA-141437. doi:10.1021/acs.analchem.9b01248
Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples
Burnum-Johnson K.E., X. Zheng, J.N. Dodds, J. Ash, D. Fourches, C.D. Nicora, and J.P. Wendler, et al. 2019. "Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples." Trends in Analytical Chemistry. TrAC 116. PNNL-SA-140985. doi:10.1016/j.trac.2019.04.022
Carrier-Assisted Single-Tube Processing Approach for Targeted Proteomics Analysis of Low Numbers of Mammalian Cells
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