Collaborative research projects in the PNNL NIH NCRR P41 Biomedical Technology Research Center 'Proteomics research resource for integrative biology'
EMSL Project ID
48135
Abstract
Abstract
Collaborative research projects in the PNNL NIH NCRR P41 Biomedical Technology Research Center 'Proteomics research resource for integrative biology'
Project Details
Start Date
2013-10-16
End Date
2016-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Alexeev Y, D Fedorov, and AA Shvartsburg. 2014. "Effective Ion Mobility Calculations for Macromolecules by Scattering off Electron Clouds." Journal of Physical Chemistry A 118:6763-6772. doi:10.1021/jp505012c
Baker ES, KE Burnum-Johnson, YM Ibrahim, DJ Orton, ME Monroe, RT Kelly, RJ Moore, X Zhang, R Theberge, CE Costello, and RD Smith. 2015. "Enhancing Bottom-up and Top-down Proteomic Measurements with Ion Mobility Separations." Proteomics. doi:10.1002/pmic.201500048
Burnum-Johnson KE, S Nie, CP Casey, ME Monroe, DJ Orton, YM Ibrahim, MA Gritsenko, TRW Clauss, AK Shukla, RJ Moore, SO Purvine, T Shi, W Qian, T Liu, ES Baker, and RD Smith. 2016. "Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Molecular and Cellular Proteomics 15(12):3694-3705. doi:10.1074/mcp.M116.061143
Chen TC, IK Webb, SA Prost, MB Harrer, RV Norheim, K Tang, YM Ibrahim, and RD Smith. 2014. "Rectangular Ion Funnel (RIF): A New Ion Funnel Interface for Structures for Lossless Ion Manipulations (SLIM)." Analytical Chemistry. doi:10.1021/ac503564c
Chen TC, TL Fillmore, SA Prost, RJ Moore, YM Ibrahim, and RD Smith. 2015. "An Orthogonal Injection Ion Funnel Interface Providing Enhanced Performance for Selected Reaction Monitoring-Triple Quadruple Mass Spectrometry." Analytical Chemistry. doi:10.1021/acs.analchem.5b01482
Chen TC, YM Ibrahim, IK Webb, VBS Garimella, X Zhang, AM Hamid, L Deng, WE Karnesky, SA Prost, JA Sandoval, RV Norheim, GA Anderson, AV Tolmachev, ES Baker, and RD Smith. 2016. "Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations." Analytical Chemistry 88(3):1728-1733. doi:10.1021/acs.analchem.5b03910
Chen Y, FE Leach, III, NK Kaiser, X Dang, YM Ibrahim, RV Norheim, GA Anderson, RD Smith, and AG Marshall. 2015. "Improved Ion Optics for Introduction of Ions into a 9.4 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer." Journal of Mass Spectrometry 50(1):280-284. doi:10.1002/jms.3523
Cox JT, I Marginean, RD Smith, and K Tang. 2014. "On the Ionization and Ion Transmission Efficiencies of Different ESI-MS Interfaces." Journal of the American Society for Mass Spectrometry . doi:10.1007/s13361-014-0998-5 [In Press]
Deng L, YM Ibrahim, AM Hamid, VBS Garimella, IK Webb, X Zheng, SA Prost, JA Sandoval, RV Norheim, GA Anderson, AV Tolmachev, ES Baker, and RD Smith. 2016. "Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13-m Serpentine Path Length Structures for Lossless Ion Manipulations Module." Analytical Chemistry. doi:10. 1021/acs. analchem. 6b01915
Deng L, YM Ibrahim, ES Baker, NA Aly, AM Hamid, X Zhang, X Zheng, VBS Garimella, IK Webb, SA Prost, JA Sandoval, RV Norheim, GA Anderson, AV Tolmachev, and RD Smith. 2016. "Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry." ChemistrySelect 1(10):2396-2399. doi:10. 1002/slct. 201600460
Depuydt GG, F Xie, VA Petyuk, A Smolders, HM Brewer, DG Camp, II, RD Smith, and BP Braeckman. 2014. "LC-MS Proteomics Analysis of the Insulin/IGF-1 Deficient C. elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism." Journal of Proteome Research. doi:dx.doi.org/pr401081b
Duan J, VK Kodali, MJ Gaffrey, J Guo, RK Chu, DG Camp, II, RD Smith, BD Thrall, and W Qian. 2015. "Quantitative Profiling of Protein S-Glutathionylation Reveals Redox-Dependent Regulation of Macrophage Function During Nanoparticle-Induced Oxidative Stress." ACS Nano Epub ahead of print:, doi:10.1021/acsnano.5b05524
Fujimoto GM, LM Rodriguez, B MacLean, RD Smith, M MacCoss, and SH Payne. 2013. "Accounting for population variation in targeted proteomics." Journal of Proteome Research 13(1):321-323. doi:10.1021/pr4011052
Garimella VBS, YM Ibrahim, IK Webb, AB Ipsen, TC Chen, AV Tolmachev, ES Baker, GA Anderson, and RD Smith. 2015. "ION MANIPULATIONS IN STRUCTURES FOR LOSSLESS ION MANIPULATIONS (SLIM): COMPUTATIONAL EVALUATION OF A 90o TURN AND A SWITCH." Analyst 140(20):6845-6852. doi:10.1039/c5an00844a
Garimella VBS, YM Ibrahim, IK Webb, AV Tolmachev, X Zhang, SA Prost, GA Anderson, and RD Smith. 2014. "Simulation of Electric Potentials and Ion Motion in Planar Electrode Structures for Lossless Ion Manipulations (SLIM)." Journal of the American Society for Mass Spectrometry 25(11):1890-6. doi:10.1007/s13361-014-0976-y
Gibbons BC, MC Chambers, ME Monroe, DL Tabb, and SH Payne. 2015. "Correcting systematic bias and instrument measurement drift with mzRefinery." Bioinformatics 31(23):3838-3840. doi:10.1093/bioinformatics/btv437
Guo X, TL Fillmore, Y Gao, and K Tang. 2016. "Capillary Electrophoresis-nanoelectrospray Ionization-selected Reaction Monitoring Mass Spectrometry Via A True Sheathless Metal-coated Emitter Interface For Robust And High Sensitivity Sample Quantification." Analytical Chemistry 88(8):4418-4425. doi:10.1021/acs.analchem.5b04912
Hamid AM, VBS Garimella, YM Ibrahim, L Deng, X Zheng, IK Webb, GA Anderson, SA Prost, RV Norheim, AV Tolmachev, ES Baker, and RD Smith. 2016. "Achieving high resolution ion mobility separations using traveling waves in compact multi-turn Structures for Lossless Ion Manipulations modules." Analytical Chemistry. doi:10. 1021/acs. analchem. 6b01914
Hamid AM, YM Ibrahim, VBS Garimella, IK Webb, L Deng, TC Chen, GA Anderson, SA Prost, RV Norheim, AV Tolmachev, and RD Smith. 2015. "Characterization of Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations." Analytical Chemistry. doi:10.1021/acs.analchem.5b02481
Hasin-Brumshtein Y, AH Khan, F Hormozdiari, C Pan, B Parks, VA Petyuk, PD Piehowski, A Bruemmer, M Pellegrini, X Xiao, E Eskin, RD Smith, AJ Lusis, and DJ Smith. 2016. "Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes." eLife 2016(5):e15614. doi:10.7554/eLife.15614
Huang EL, PD Piehowski, DJ Orton, RJ Moore, W Qian, CP Casey, X Sun, SK Dey, KE Burnum-Johnson, and RD Smith. 2016. "SNaPP: Simplified Nano-Proteomics Platform for reproducible global proteomic analysis of nanogram protein quantities." Endocrinology . doi:10.1210/en.2015-1821 [In Press]
Ibrahim YM, ES Baker, WF Danielson Iii, RV Norheim, DC Prior, GA Anderson, ME Belov, and RD Smith. "Development of a new ion mobility (quadrupole) time-of-flight mass spectrometer." International Journal of Mass Spectrometry. doi:10.1016/j.ijms.2014.07.034
Ibrahim YM, VBS Garimella, AV Tolmachev, ES Baker, and RD Smith. 2014. "Improving Ion Mobility Measurement Sensitivity by Utilizing Helium in an Ion Funnel-Trap." Analytical Chemistry Epub ahead of print:, doi:10.1021/ac404250z
Jonkers W, AC Leeder, C Ansong, Y Wang, F Yang, TL Starr, DG Camp, II, RD Smith, and NL Glass. 2014. "HAM-5 functions as a MAP kinase scaffold during cell fusion in Neurospora crassa." PLoS Genetics 10(11):Article No. e1004783. doi:10.1371/journal.pgen.1004783
Kebaabetswe LP, AK Haick, MA Gritsenko, TL Fillmore, RK Chu, SO Purvine, BJM Webb-Robertson, MM Matzke, RD Smith, KM Waters, TO Metz, and TA Miura. 2015. "Proteomic Analysis Reveals Down-Regulation of Surfactant Protein B in Murine Type II Pneumocytes Infected with Influenza A Virus." Virology 438:96-107. doi:10.1016/j.virol.2015.03.045
Kramer PA, J Duan, W Qian, and DJ Marcinek. 2015. "The measurement of reversible redox dependent post-translational modifications and their regulation of mitochondrial and skeletal muscle function." Frontiers in Physiology 6:347-1 to 347-14. doi:10.3389/fphys.2015.00347
Kyle JE, X Zhang, KK Weitz, ME Monroe, YM Ibrahim, RJ Moore, J Cha, X Sun, ES Lovelace, J Wagoner, S Polyak, TO Metz, SK Dey, RD Smith, KE Burnum-Johnson, and ES Baker. 2016. "Uncovering Biologically Significant Lipid Isomers with Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Analyst . doi:10.1039/C5AN02062J [In Press]
Li J, ES Nakayasu, CC Overall, R Johnson, AS Kidwai, JE McDermott, C Ansong, F Heffron, E Cambronne, and JN Adkins. 2015. "Global analysis of Salmonella alternative sigma factor E on protein translation." Journal of Proteome Research 14(4):1716-1726. doi:10.1021/pr5010423
Nicora C.D., K.E. Burnum-Johnson, E.S. Nakayasu, C.P. Casey, R.A. White, T. Roy Chowdhury, and J.E. Kyle, et al. 2018. "The MPLEx Protocol for Multi-Omic Analyses of Soil Samples." Journal of Visualized Experiments e57343, no. 135. PNNL-SA-129344. doi:10.3791/57343
Park JK, PD Piehowski, CS Wilkins, M Zhou, JA Mendoza, GM Fujimoto, Y Shen, AK Shukla, RJ Moore, T Liu, VA Petyuk, N Tolic, L Pasa Tolic, RD Smith, SH Payne, and S Kim. 2017. "Informed-Proteomics: Open Source Software Package for Top-down Proteomics." Nature Methods 14:909-914. doi:10.1038/nmeth.4388
Perez DM, ME Richards, R Parker, ME Berres, AT Wright, M Sifri, NC Sadler, N Tatiyaborworntham, and N Li. 2016. "Role of cytochrome P450 hydroxylase in the decreased accumulation of vitamin E in muscle from turkeys compared to that from chickens." Journal of Agricultural and Food Chemistry 64(3):671-80. doi:10.1021/acs.jafc.5b05433
Prost SA, KL Crowell, ES Baker, YM Ibrahim, BH Clowers, ME Monroe, GA Anderson, RD Smith, and SH Payne. 2014. "Detecting and Removing Data Artifacts in Hadamard Transform Ion Mobility-Mass Spectrometry Measurements." Journal of the American Society for Mass Spectrometry Epub Ahead of print:, doi:10.1007/s13361-014-0895-y
Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea
Brown JN, HM Brewer, CD Nicora, KK Weitz, MJ Morris, AJ Skabelund, JN Adkins, RD Smith, JH Cho, and R Gelinas. 2014. "Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea." BMC Medical Genomics 7(1):58. doi:10.1186/1755-8794-7-58
Quaamari A, E Dirice, N Gedeon, J Hu, JY Zhou, J Shirakawa, L Hou, J Goodman, C Karampelias, G Qiang, J Boucher, R Martinez, MA Gritsenko, DF De Jesus, S Kahraman, S Bhatt, RD Smith, HD Beer, P Jungtrakoon, Y Gong, AB Goldfine, CW Liew, A Doria, O Andersson, W Qian, E Remold-O'Donnell, and RN Kulkami. 2016. "SerpinB1 Promotes Pancreatic ? Cell Proliferation." Cell Metabolism 23(1):194-205. doi:10.1016/j.cmet.2015.12.001
Ryu S, W Qian, DG Camp, II, RD Smith, RG Tompkins, RW Davis, and W Xiao. 2014. "Detecting differential protein expression in large-scale population proteomics." Bioinformatics 00(00):1-7. doi:10.1093/bioinformatics/btu341
Shin AC, M Fasshauer, N Filatova, LA Grundell, E Zielinski, J Zhou, T Scherer, C Lindtner, PJ White, AL Lapworth, O Llkayeva, U Knippschild, AM Wolf, L Scheja, KL Grove, RD Smith, W Qian, CJ Lynch, CB Newgard, and C Buettner. 2014. "Brain insulin lowers circulating BCAA levels by inducing hepatic BCAA catabolism ." Cell Metabolism. doi:10.1016/j.cmet.2014.09.003 [In Press]
Shi T, SI Quek, Y Gao, CD Nicora, S Nie, TL Fillmore, T Liu, KD Rodland, RD Smith, R Leach, IM Thompson, EA Vitello, WJ Ellis, AY Liu, and W Qian. 2017. "Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins." Oncotarget 8(60):101887-101898. doi:10.18632/oncotarget.21710
Shvartsburg AA. 2014. "Ultrahigh-Resolution Differential Ion Mobility Separations of Conformers for Proteins above 10 kDa - Onset of Dipole Alignment?" Analytical Chemistry . doi:10.1021/ac502389a [In Press]
Shvartsburg AA, YM Ibrahim, and RD Smith. 2014. "Differential Ion Mobility Separations in up to 100% Helium Using Microchips." Journal of the American Society for Mass Spectrometry 2014(25):480-489. doi:10.1007/s13361-013-0797-4
Sigdel TK, CD Nicora, SC Hsieh, H Dai, W Qian, DG Camp, II, and MM Sarwal. 2014. "Optimization for Peptide Sample Preparation for Urine Peptidomics." Clinical Proteomics 11:Article No. 7. doi:10.1186/1559-0275-11-7
Sigdel TK, Y Gao, J He, A Wang, CD Nicora, TL Fillmore, T Shi, BJM Webb-Robertson, RD Smith, W Qian, O Salvatierra, DG Camp, II, and M Sarwal. 2016. "Mining the Human Urine Proteome for Monitoring Renal Transplant Injury ." Kidney International 89(6):1244-1252. doi:10. 1016/j. kint. 2015. 12. 049
Sigdel TK, Y NG, S Lee, CD Nicora, W Qian, RD Smith, DG Camp, II, and MM Sarwal. 2015. "Perturbations in the Urinary Exosome in Transplant Rejection." Frontiers of Medicine 1(57):, doi:10.3389/fmed.2014.00057
Tolmachev AV, IK Webb, YM Ibrahim, VBS Garimella, X Zhang, GA Anderson, and RD Smith. 2014. "Characterization of Ion Dynamics in Structures for Lossless Ion Manipulations." Analytical Chemistry epub ahead of print:, doi:10.1021/ac502054p
Vrablik TL, VA Petyuk, EM Larson, RD Smith, and J Watts. 2015. " Q21Q1 Lipidomic and proteomic analysis of Caenorhabditis elegans lipid droplets and identi?cation of ACS-4 as a lipid droplet-associated protein ." Biochimica and Biophysica Acta. Molecular and Cell Biology of Lipids. . doi:10.1016/j.bbalip.2015.06.004 [In Press]
Wang S, F Yang, VA Petyuk, AK Shukla, ME Monroe, MA Gritsenko, KD Rodland, RD Smith, W Qian, CX Gong, and T Liu. 2017. "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease." The Journal of Pathology 243(1):78-88. doi:10.1002/path.4929
Waters E M,Rudkin J K,Clair GCD ,Adkins J N,Gore S ,Xia G ,Black N S,Downing T ,O'Neill E ,Kadioglu A ,O'Gara J P 2016. "Redeploying ?-lactam antibiotics as a novel anti-virulence strategy for the treatment of MRSA infections" The journal of Infectious Disease ePub():. 10.1093/infdis/jiw461
Webb IK, VBS Garimella, AV Tolmachev, TC Chen, X Zhang, JT Cox, RV Norheim, SA Prost, BL Lamarche, GA Anderson, YM Ibrahim, and RD Smith. 2014. "Mobility-Resolved Ion Selection in Uniform Drift Field Ion Mobility Spectrometry/Mass Spectrometry; Dynamic Switching in Structures for Lossless Ion Manipulations ." Analytical Chemistry epub ahead of print:, doi:10.1021/ac502139e
Webb IK, VBS Garimella, AV Tolmachev, TC Chen, X Zhang, RV Norheim, SA Prost, BL Lamarche, GA Anderson, YM Ibrahim, and RD Smith. 2014. "Experimental Evaluation and Optimization of Structures for Lossless Ion Manipulations for Ion Mobility Spectrometry/Time-of-Flight Mass Spectrometry." Analytical Chemistry Epub ahead of print:, doi:10.1021/ac502055e
Webb IK, VBS Garimella, RV Norheim, ES Baker, YM Ibrahim, and RD Smith. 2016. "A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation." Journal of the American Society for Mass Spectrometry 2016(27):1285-1288. doi:10.1007/s13361-016-1397-x
Wojcik R, IK Webb, VBS Garimella, SA Prost, YM Ibrahim, EM Baker, and RD Smith. 2017. "Lipid and Glycolipid Isomer Analyses Using Ultra-high Resolution Ion Mobility Spectrometry Separations." International Journal of Molecular Sciences 18(1):183. doi:10.3390/ijms18010183
Woo S, S Cha Won, S Na, C Guest, T Liu, RD Smith, KD Rodland, SH Payne, and V Bafna. 2014. "Proteogenomic strategies for identification of aberrant cancer peptides using large-scale Next Generation Sequencing data." Proteomics epub ahead of print:, doi:10.1002/pmic.201400206
Wu C, J Duan, T Liu, RD Smith, and W Qian. 2016. "Contributions of Immunoaffinity Chromatography to Deep Proteome Profiling of Human Biofluids." Journal of Chromatography B. doi:10.1016/j.jchromb.2016.01.015
Wu C, ME Monroe, Z Xu, GW Slysz, SH Payne, KD Rodland, T Liu, and RD Smith. 2015. "An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics." Journal of the American Society for Mass Spectrometry . doi:10.1007/s13361-015-1169-z [In Press]
Xiong Y, ST Coradetti, X Li, MA Gritsenko, TRW Clauss, VA Petyuk, DG Camp, II, RD Smith, JH Cate, F Yang, and L Glass. 2014. "The proteome and phosphoproteome of Neurospora crassa in response to cellulose, sucrose and carbon starvation." Fungal Genetics and Biology : FG & B. doi:10.1016/j.fgb.2014.05.005 [Epub ahead of print]
Zhang H, T Liu, Z Zhang, SH Payne, B Zhang, JE McDermott, JY Zhou, VA Petyuk, L Chen, D Ray, S Sun, F Yang, L Chen, J Wang, P Shah, SW Cha, P Aiyetan, S Woo, Y Tian, MA Gritsenko, TRW Clauss, C Choi, ME Monroe, SN Thomas, S Nie, C Wu, RJ Moore, KH Yu, DL Tabb, D Fenyo, V Bafna, Y Wang, H Rodriguez, E Boja, T Hiltket, R Rivers, LJ Sokoll, H Zhu, IM Shih, L Cope, A Pandey, B Zhang, M Snyder, D Levine, RD Smith, DW Chan, and KD Rodland. 2016. "Integrated proteogenomic characterization of human high grade serous ovarian cancer." Cell 166(3):755-765. doi:10. 1016/j. cell. 2016. 05. 069
Zhang X., M.V. Romm, X. Zheng, E.M. Zink, Y. Kim, K.E. Burnum-Johnson, and D.J. Orton, et al. 2016. "SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in bio?uids." Clinical Mass Spectrometry 2. PNNL-SA-117436. doi:10.1016/j.clinms.2016.11.002
Zhang X, VBS Garimella, SA Prost, IK Webb, TC Chen, K Tang, AV Tolmachev, RV Norheim, ES Baker, GA Anderson, YM Ibrahim, and RD Smith. 2015. "Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations ." Analytical Chemistry 87(12):6010-6016. doi:10.1021/acs.analchem.5b00214
Zheng X, X Zhang, N Schocker, RS Renslow, DJ Orton, J Khamsi, RA Ashmus, IC Almeida, K Tang, CE Costello, RD Smith, K Michael, and EM Baker. 2017. "Enhancing Glycan Isomer Separations with Metal Ions and Positive and Negative Polarity Ion Mobility Spectrometry-Mass Spectrometry Analyses." Analytical and Bioanalytical Chemistry 409:467-476. doi:10.1007/s00216-016-9866-4