Collaborative research projects in the PNNL NIH NCRR P41 Biomedical Technology Research Center 'Proteomics research resource for integrative biology'
EMSL Project ID
40072
Abstract
Collaborative research projects in the PNNL NIH NCRR P41 Biomedical Technology Research Center 'Proteomics research resource for integrative biology'
Project Details
Start Date
2010-10-01
End Date
2013-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Adkins JN, H Mottaz, TO Metz, CK Ansong, NP Manes, RD Smith, and F Heffron. 2010. "Performing Comparative Peptidomics Analyses of Salmonella from Different Growth Conditions." Chapter 2 in Peptidomics: Methods and Protocols, Methods in Molecular Biology, vol. 615, ed. Mikhail Soloviev, pp. 13-27. Humana Press, Inc., New York, NY.
Alfaro JF, CX Gong, ME Monroe, JT Aldrich, TRW Clauss, SO Purvine, Z Wang, DG Camp, II, J Shabanowitz, P Stanley, GW Hart, DF Hunt, F Yang, and RD Smith. 2012. "Tandem Mass Spectrometry identifies novel mouse brain O-GlcNAcylated proteins including targets of the ER-resident O-GlcNAc transferase." Proceedings of the National Academy of Sciences of the United States of America 109(19):7280-7285. doi:10.1073/pnas.1200425109
Andreev VP, VA Petyuk, HM Brewer, Y Karpievitch, F Xie, J Clarke, DG Camp, II, RD Smith, AP Lieberman, RL Albin, Z Nawaz, JE Hokayem, and AJ Myers. 2012. "Label-Free Quantitative LC?MS Proteomics of Alzheimer’s Disease and Normally Aged Human Brains." Journal of Proteome Research 11(6):3053-3067. doi:10.1021/pr3001546
Angel TE, BJ Luft, X Yang, CD Nicora, DG Camp, II, JM Jacobs, and RD Smith. 2010. "Proteome Analysis of Borrelia burgdorferi Response to Environmental Change." PLoS One 5(11):Article No.: e13800. doi:10.1371/journal.pone.0013800
Angel TE, JM Jacobs, S Elias, MA Gritsenko, AK Shukla, DG Camp, II, MS Pasternack, C McCarthy, RP Smith, S Warren, and RD Smith. 2012. "Cerebrospinal fluid proteome of subjects with acute Lyme disease." Journal of Proteome Research 11(10):4814-22. doi:10.1021/pr300577p
Angel TE, JM Jacobs, SS Spudich, MA Gritsenko, D Fuchs, T Liegler, H Zetterberg, DG Camp, II, RW Price, and RD Smith. 2012. "The cerebrospinal fluid proteome in HIV infection: change associated with disease severity." Clinical Proteomics 9:Article No. 3. doi:10.1186/1559-0275-9-3
Angel TE, UK Aryal, SM Hengel, ES Baker, RT Kelly, EW Robinson, and RD Smith. 2012. "Mass spectrometry-based proteomics: existing capabilities and future directions." Chemical Society Reviews 41(10):3912-3928. doi:10.1039/C2CS15331A
Ansong C, C Ortega, SH Payne, DH Haft, LM Chauvigne-Hines, MP Lewis, SO Purvine, AK Shukla, S Fortuin, RD Smith, JN Adkins, C Grundner, and AT Wright. 2013. "Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis." Chemistry & Biology 20(1):123-133. doi:10.1016/j.chembiol.2012.11.008
Belov ME, S Prasad, DC Prior, WF Danielson, III, KK Weitz, YM Ibrahim, and RD Smith. 2011. "Pulsed Multiple Reaction Monitoring Approach to Enhancing Sensitivity of a Tandem Quadrupole Mass Spectrometer." Analytical Chemistry 83(6):2162–2171. doi:10.1021/ac103006b
Brown JN, GM Ortiz, TE Angel, JM Jacobs, MA Gritsenko, EY Chan, DE Purdy, RD Murnane, K Larsen, RE Palermo, AK Shukla, TRW Clauss, MG Katze, JM McCune, and RD Smith. 2012. "Morphine Produces Immunosuppressive Effects in Non-human Primates at the Proteomic and Cellular Levels." Molecular & Cellular Proteomics. MCP. doi:10.1074/mcp.M111.016121
Buchko GW, G Niemann, ES Baker, ME Belov, RD Smith, F Heffron, JN Adkins, and JE McDermott. 2010. "A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins." Molecular Biosystems 6(12):2448-2458. doi:10.1039/c0mb00097c
Charusanti P, S Chauhan, K Mcateer, JA Lerman, DR Hyduke, VL Motin, C Ansong, JN Adkins, and BO Palsson. 2011. "An Experimentally-Supported Genome-Scale Metabolic Network Reconstruction for Yersinia pestis CO92." BMC Systems Biology 5:Article No. 163. doi:10.1186/1752-0509-5-163
Chauvigne-Hines LM, LN Anderson, HM Weaver, JN Brown, PK Koech, CD Nicora, BA Hofstad, RD Smith, MJ Wilkins, SJ Callister, and AT Wright. 2012. "Suite of Activity-Based Probes for Cellulose-Degrading Enzymes." Journal of the American Chemical Society 134(50):20521-20532. doi:10.1021/ja309790w
Chauvin T, F Xie, T Liu, CD Nicora, F Yang, DG Camp, II, RD Smith, and KP Roberts. 2012. "A Systematic Analysis of a Deep Mouse Epididymal Sperm Proteome." Biology of Reproduction 87(6):141. doi:10.1095/biolreprod.112.104208
Crowell KL, GW Slysz, ES Baker, BL Lamarche, ME Monroe, YM Ibrahim, SH Payne, GA Anderson, and RD Smith. 2013. "LC-IMS-MS Feature Finder: Detecting Multidimensional Liquid Chromatography, Ion Mobility, and Mass Spectrometry Features in Complex Datasets." Bioinformatics 29(21):2804-2805 . doi:10.1093/bioinformatics/btt465
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 Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism." Journal of Proteome Research. doi:10.1021/pr401081b
Depuydt GG, F Xie, VA Petyuk, N Shanmugam, A Smolders, I Dhondt, HM Brewer, DG Camp, II, RD Smith, and BP Braeckman. 2014. "Reduced insulin/IGF?1 signaling and dietary restriction inhibit translation but preserve muscle mass in Caenorhabditis elegans." Molecular and Cellular Proteomics. doi:10.1074/mcp.M113.027383 mcp.M113.027383
Diamond DL, AJ Syder, JM Jacobs, CM Sorensen, KA Walters, S Proll, JE McDermott, MA Gritsenko, Q Zhang, R Zhao, TO Metz, DG Camp, II, KM Waters, RD Smith, CM Rice, and MG Katze. 2010. "Temporal Proteome and Lipidome Profiles Reveal HCV-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics ." PLoS Pathogens 6(1):Art. No. e1000719. doi:10.1371/journal.ppat.1000719
Diamond DL, A Krasnoselski, KE Burnum, ME Monroe, BJM Webb-Robertson, JE McDermott, MM Yeh, S Strom , S Proll, S Belisle, A Rasmussen, KA Walters, JM Jacobs, MA Gritsenko, DG Camp, II, R Bhattacharya, JD Perkins, RL Carithers, IW Liou, AM Larson, KM Waters, RD Smith, and MG Katze. 2012. "Proteome and Computational Analyses Reveal New Insights into the Mechanisms of Hepatitis C Virus Mediated Liver Disease Post-Transplantation." Hepatology. doi:10.1002/hep.25649 (Epub ahead of print)
Dresang LR, JR Teuton, F Huichen, JM Jacobs, DG Camp, II, SO Purvine, MA Gritsenko, L Zhihua, RD Smith, B Sugden, PS Moore, and Y Chang. 2011. "Coupled Transcriptome and Proteome Analysis of Human Lymphotropic Tumor Viruses: Insights on the Detection and Discovery of Viral Genes." BMC Genomics 12:625.
Finnerty CC, MG Jeschke, W Qian, A Kaushal, W Xiao, T Liu, MA Gritsenko, RJ Moore, DG Camp, II, LL Moldawer, C Elson, D Schoenfeld, R Gamelli, N Gibran, M Klein, B Arnoldo, D Remick, RD Smith, RW Davis, RG Tompkins, and DN Herndon. 2013. "DETERMINATION OF BURN PATIENT OUTCOME BY LARGE SCALE QUANTITATIVE DISCOVERY PROTEOMICS." Critical Care Medicine. doi:10.1097/CCM.0b013e31827c072e
Frank AM, ME Monroe, AR Shah, JJ Carver, N Bandeira, RJ Moore, GA Anderson, RD Smith, and PA Pevzner. 2011. "Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra." Nature Methods 8(7):587-591. doi:10.1038/nmeth.1609
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 87(22):11301-11308. doi:10.1021/acs.analchem.5b02481
Hengel SM, EA Floyd, ES Baker, R Zhao, S Wu, and L Pasa-Tolic. 2012. "Evaluation of SDS depletion using an affinity spin column and IMS-MS detection." Proteomics 12(21):3138-3142. doi:10.1002/pmic.201200168
Hyung SW, RJ Moore, PD Piehowski, DJ Orton, AA Schepmoes, TRW Clauss, RK Chu, TL Fillmore, HM Brewer, T Liu, R Zhao, and RD Smith. 2014. "Micro-Scale Depletion of High Abundance Proteins in Human Bio-fluids using IgY14 Immunoaffinity Resin: Analysis of Human Plasma and Cerebrospinal Fluid ." Journal of Proteome Research Epub ahead of print:, doi:10.1007/s00216-014-8058-3
Jun SH, MS Chang, BC Kim, HJ An, D Lopez-Ferrer, R Zhao, RD Smith, SW Lee, and J Kim. 2010. "Trypsin coatings on electrospun and alcohol-dispersed polymer nanofibers for trypsin digestion column." Analytical Chemistry 82(18):7828 - 7834. doi:10.1021/ac101633e
Karpievitch YV, AD Polpitiya, GA Anderson, RD Smith, and AR Dabney. 2010. "Liquid Chromatography Mass Spectrometry-Based Proteomics: Biological and Technological Aspects." The Annals of Applied Statistics 4(4):1797-1823.
Kelly RT, AV Tolmachev, JS Page, K Tang, and RD Smith. 2010. "The Ion Funnel: Theory, Implementations and Applications." Mass Spectrometry Reviews 29(2):294-312. doi:10.1002/mas.20232
Kim JS, ME Monroe, DG Camp, II, RD Smith, and W Qian. 2013. "In-Source Fragmentation and the Sources of Partially Tryptic Peptides in Shotgun Proteomics ." Journal of Proteome Research 12(2):910-916. doi:10.1021/pr300955f.Epub 2013 January 16.
Kim JS, TL Fillmore, T Liu, EW Robinson, M Hossain, BL Champion, RJ Moore, DG Camp, II, RD Smith, and W Qian. 2011. "18O-Labeled Proteome Reference as Global Internal Standards for Targeted Quantification by Selected Reaction Monitoring-Mass Spectrometry." Molecular & Cellular Proteomics. MCP 10(12):Article No. M110.007302. doi:10.1074/mcp.M110.007302
Kim JS, Z Dai, UK Aryal, RJ Moore, DG Camp, II, SE Baker, RD Smith, and W Qian. 2013. "Resin-assisted Enrichment of N-terminal Peptides for Characterizing Proteolytic Processing ." Analytical Chemistry 85(14):6826-6832. doi:10.1021 /ac401000q
Kuta J, Z Wang, K Wisuri, MCF Wander, N Wall, and AE Clark. 2013. "The surface structure of ?-uranophane and its interaction with Eu(III) – An integrated computational and fluorescence spectroscopy study." Geochimica et Cosmochimica Acta 103:184-196. doi:10.1016/j.gca.2012.10.056
Lee JH, SW Hyung, DG Mun, HJ Jung, H Kim, H Lee, SJ Kim, KS Park, RJ Moore, RD Smith, and SW Lee. 2012. "A fully automated multi-functional ultrahigh pressure liquid chromatography system for advanced proteome analyses." Journal of Proteome Research 11(8):4373-4381.
Lopez-Ferrer D, K Petritis, EW Robinson, KK Hixson, Z Tian, JH Lee, SW Lee, N Tolic, KK Weitz, ME Belov, RD Smith, and L Pasa-Tolic. 2011. "Pressurized Pepsin Digestion in Proteomics: An Automatable Alternative to Trypsin for Integrated Top-down Bottom-up Proteomics." Molecular & Cellular Proteomics. MCP 10(2):, doi:10.1074/mcp.M110.001479
Malouli D, ES Nakayasu, K Viswanathan, DG Camp, II, WL Chang, PA Barry, RD Smith, and K Fruh. 2012. "Re-evaluation of the coding potential and proteomic analysis of the BAC derived Rhesus cytomegalovirus strain 68-1." PNNL-SA-87442, Pacific Northwest National Laboratory, Richland, WA. [Unpublished]
Marginean I, SR Kronewitter, RJ Moore, GW Slysz, ME Monroe, GA Anderson, K Tang, and RD Smith. 2012. "Improving N-Glycan Coverage using HPLC-MS with Electrospray Ionization at Subambient Pressure." Analytical Chemistry 84(21):9208-9213. doi:10.1021/ac301961u
Maxwell E, Y Tan, Y Tan, H Hu, G Benson, K Aizikov, S Conley, GO Staples, GW Slysz, RD Smith, and J Zaia. 2012. "GlycReSoft: A Software Package for Automated Recognition of Glycans from LC/MS Data ." PLoS One 7(9):e45474. doi:10.1371/journal.pone.0045474
Merkley ED, ES Baker, KL Crowell, DJ Orton, T Taverner, C Ansong, YM Ibrahim, MC Burnet, JR Cort, GA Anderson, RD Smith, and JN Adkins. 2013. "Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein-Protein Interactions by Chemical Cross-Linking ." Journal of the American Society for Mass Spectrometry. doi:10.1007/s13361-012-0565-x
Merkley ED, TO Metz, RD Smith, J Baynes, and N Frizell. 2014. "The Succinated Proteome." Mass Spectrometry Reviews [Epub ahead of print]:, doi:10.1002/mas.21382
Nakayasu ES, C Ansong, JN Brown, F Yang, D Lopez-Ferrer, W Qian, RD Smith, and JN Adkins. 2013. "Evaluation of selected binding domains for the analysis of ubiquitinated proteomes." Journal of the American Society for Mass Spectrometry. doi:10.1007/s13361-013-0619-8. Epub ahead of print
Ortega C, R Liao, LN Anderson, T Rustad, AR Ollodart, AT Wright, DR Sherman, and C Grundner. 2014. "Mycobacterium tuberculosis Ser/Thr protein kinase B mediates an oxygen-dependent replication switch." PLoS Biology 12(1):Article No. e1001746. doi:10.1371/journal.pbio.1001746
Piehowski PD, VA Petyuk, DJ Orton, F Xie, RJ Moore, M Ramirez, A Engel, AP Lieberman, RL Albin, DG Camp, II, RD Smith, and AJ Myers. 2013. "Sources of Technical Variability in Quantitative LC-MS Proteomics: Human Brain Tissue Sample Analysis." Journal of Proteome Research 12(5):2128-2137. doi:10.1021/pr301146m. Epub 2013 April 10.
Piehowski PD, VA Petyuk, JD Sandoval, KE Burnum, GR Kiebel, ME Monroe, GA Anderson, DG Camp, II, and RD Smith. 2013. "STEPS: A Grid Search Methodology for Optimized Peptide Identification Filtering of MS/MS Database Search Results." Proteomics 13(5):766-770. doi:10.1002/pmic.201200096
Pincus DE, C Ryan, RD Smith, R Brent, and O Resnekov. 2013. "Assigning quantitative function to post-Â?translational modifications reveals multiple sites of phosphorylation that tune yeast pheromone signaling output." PLoS One 8(3):Article No. e56544. doi:10.1371/journal.pone.0056544
Qian W, BO Petritis, A Kaushal, CC Finnerty, MG Jescheke, ME Monroe, RJ Moore, AA Schepmoes, W Xiao, LL Moldawer, RW Davis, RG Tompkins, DN Herndon, DG Camp, II, and RD Smith. 2010. "Plasma Proteome Response to Severe Burn Injury Revealed by 18O-Labeled “Universal” Reference-based Quantitative Proteomics." Journal of Proteome Research 9(9):4779-4789.
Rutledge AC, G Fontes, MA Gritsenko, AD Norbeck, DJ Anderson, KM Waters, JN Adkins, RD Smith, V Poitout, and TO Metz. 2012. "Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics." Journal of Biological Chemistry. doi:10.1021/pr3002996
Schoenherr RM, KS Kelly-Spratt, CW Lin, JR Whiteaker, T Liu, T Holzman, I Coleman, LC Feng, TD Lorentzen, AL Krasnoselsky, P Wang, Y Liu, KE Gurley, LM Amon, AA Schepmoes, RJ Moore, DG Camp, II, LA Chodosh, RD Smith, PS Nelson, M McIntosh, C Kemp, and AG Paulovich. 2011. "Proteome and Transcriptome Profiles of a Her2/Neu-driven Mouse Model of Breast Cancer." Proteomics - Clinical Applications 5(3-4):179-188. doi:10.1002/prca.201000037
Shen Y, N Tolic, SO Purvine, and RD Smith. 2011. "Improving CID, HCD, and ETD FT MS/MS degradome-peptidome identifications using high accuracy mass information." Journal of Proteome Research. doi:10.1021/pr200597j
Shen Y, T Liu, N Tolic, BO Petritis, R Zhao, RJ Moore, SO Purvine, DG Camp, II, and RD Smith. 2010. "A strategy for degradomic-peptidomic analysis of the human blood plasma ." Journal of Proteome Research 9(5):2339-2346. doi:10.1021/pr901083m
Shi T, TL Fillmore, X Sun, R Zhao, AA Schepmoes, M Hossain, S Wu, JS Kim, NJ Jones, RJ Moore, L Pasa-Tolic, J Kagan, KD Rodland, T Liu, K Tang, DG Camp, II, RD Smith, and W Qian. 2012. "An antibody-free, targeted mass spectrometry approach for quantification of proteins at low picogram/milliliter levels in human plasma/serum." Proceedings of the National Academy of Sciences of the United States of America. doi:10.1073/pnas.1204366109 [In Press]
Shi T, Y Gao, SI Quek, TL Fillmore, CD Nicora, D Su, R Zhao, KD Rodland, T Liu, RD Smith, DW Chan, DG Camp, II, AY Liu, and W Qian. 2013. "A highly sensitive targeted mass spectrometric assay for quantification of low-abundance AGR2 in human urine and serum." Journal of Proteome Research. doi:10.1021/pr400912c [Epub Ahead of Print]
Shi T, Y Gao, SI Quek, TL Fillmore, CD Nicora, D Su, R Zhao, KD Rodland, T Liu, RD Smith, DW Chan, DG Camp, II, AY Liu, and W Qian. 2014. "A highly sensitive targeted mass spectrometric assay for quantification of low-abundance AGR2 in human urine and serum." Journal of Proteome Research 13(2):875-882. doi:10.1021/pr400912c
Shvartsburg AA, A Creese, RD Smith, and HJ Cooper. 2010. "Separation of Peptide Isomers with Variant Modified Sites by High-Resolution Differential Ion Mobility Spectrometry." Analytical Chemistry 82(19):8327-8334. doi:10.1021/ac101878a
Shvartsburg AA, and RD Smith. 2011. "Accelerated High-Resolution Differential Ion Mobility Separations Using Hydrogen ." Analytical Chemistry 83:9159-9166. doi:dx.doi.org/10.1021/ac202386w
Shvartsburg AA, and RD Smith. 2011. "Ultrahigh-Resolution Differential Ion Mobility Spectrometry Using Extended Separation Times." Analytical Chemistry 83(1):23-29. doi:10.1021/ac102689p
Shvartsburg AA, and RD Smith. 2012. "Protein Analyses Using Differential Ion Mobility Microchips with Mass Spectrometry." Analytical Chemistry. doi:dx.doi.org/10.1021/ac3018636 [In Press]
Shvartsburg AA, and RD Smith. 2013. "High-Resolution Differential Ion Mobility Spectrometry of a Protein." Analytical Chemistry 85(1):10-13. doi:10.1021/ac3029129
Shvartsburg AA, and RD Smith. 2013. "Separation of Protein Conformers by Differential Ion Mobility in Hydrogen-Rich Gases ." Analytical Chemistry 85(15):6967-6973. doi:10.1021/ac4015963
Shvartsburg AA, TA Seim, WF Danielson, III, RV Norheim, RJ Moore, RD Smith, and GA Anderson. 2013. "High-Definition Differential Ion Mobility Spectrometry with Resolving Power up to 500 ." Journal of the American Society for Mass Spectrometry 24:109-114. doi:10.1007/s13361-012-0517-5
Shvartsburg AA, Y Zheng, RD Smith, and N Kelleher. 2012. "Ion Mobility Separation of Variant Histone Tails Extending to the “Middle-down” Range ." Analytical Chemistry 84(10):4271-4276. doi:10.1021/ac300612y
Shvartsburg AA, Y Zheng, RD Smith, and N Kelleher. 2012. "Separation of Variant Methylated Histone Tails by Differential Ion Mobility ." Analytical Chemistry 84:6317-6320. doi:dx.doi.org/10.1021/ac301541r
Smith JS, TE Angel, C Chavkin, DJ Orton, RJ Moore, and RD Smith. 2014. "Characterization of individual mouse cerebrospinal fluid proteomes." Proteomics 2014(00):1-5. doi:10.1002/pmic.201300241
Smith RD. 2012. "Mass spectrometry in biomarker applications: from untargeted discovery to targeted verification, and implications for platform convergence and clinical application." Clinical Chemistry 58(3):528-530. doi:10.1373/clinchem.2011.180596
Su D, AK Shukla, B Chen, JS Kim, ES Nakayasu, Y Qu, UK Aryal, KK Weitz, TRW Clauss, ME Monroe, DG Camp, II, DJ Bigelow, RD Smith, RN Kulkarni, and W Qian. 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 57:68-78. doi:10.1016/j.freeradbiomed.2012.12.010
Sun X, RT Kelly, K Tang, and RD Smith. 2010. "Ultrasensitive Nanoelectrospray Ionization-Mass Spectrometry using Poly(dimethylsiloxane) Microchips with Monolithically Integrated Emitters." Analyst 135(9):2296-2302.
Sun X, RT Kelly, K Tang, and RD Smith. 2011. "Membrane-Based Emitter for Coupling Microfluidics with Ultrasensitive Nanoelectrospray Ionization-Mass Spectrometry." Analytical Chemistry 83(4):5797-5803. doi:10.1021/ac200960h
Taverner T, Y Karpievitch, AD Polpitiya, GA Anderson, and RD Smith. 2012. "DanteR: an extensible R-based tool for quantitative analysis of -omics data ." Bioinformatics 28(18):2404-2406.
Tian Z, R Zhao, N Tolic, RJ Moore, DL Stenoien, EW Robinson, RD Smith, and L Pasa-Tolic. 2010. "Two-dimensional liquid chromatography system for online top-down mass spectrometry." Proteomics 10(20):3610-3620. doi:10.1002/pmic.201000367
Wang L, UK Aryal, Z Dai, AC Mason, ME Monroe, Z Tian, J Zhou, D Su, KK Weitz, T Liu, DG Camp, II, RD Smith, SE Baker, and W Qian. 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(1):143-56. doi:10.1021/pr200916k
Wang X, GA Anderson, RD Smith, and AR Dabney. 2012. "A Hybrid Approach to Protein Differential Expression in Mass Spectrometry-Based Proteomics." Bioinformatics 28(12):1586-1591. doi:10.1093/bioinformatics/bts193
Wang Y, F Yang, Y Fu, X Huang, W Wang, X Jiang, MA Gritsenko, R Zhao, ME Monroe, OC Pertz, SO Purvine, DJ Orton, JM Jacobs, DG Camp, II, RD Smith, and RL Klemke. 2011. "Spatial Phosphoprotein Profiling Reveals a Compartmentalized Extracellular Signal-regulated Kinase Switch Governing Neurite Growth and Retraction." Journal of Biological Chemistry 286(20):18190-18201.
Wu S, JN Brown, N Tolic, D Meng, X Liu, H Zhang, R Zhao, RJ Moore, PA Pevzner, RD Smith, and L Pasa-Tolic. 2014. "Quantitative Analysis of Human Salivary Gland-Derived Intact Proteome Using Top-Down Mass Spectrometry." Proteomics. doi:10.1002/pmic.201300378 [In Press]
Xie F, RD Smith, and Y Shen. 2012. "Advanced proteomic liquid chromatography ." Journal of Chromatography A. doi:dx.doi.org/10.1016/j.chroma.2012.06.098
Yang F, KM Waters, BJM Webb-Robertson, MB Sowa, CH Freiin von Neubeck, JT Aldrich, LM Markillie, RM Wirgau, MA Gristenko, R Zhao, DG Camp, II, RD Smith, and DL Stenoien. 2012. "Quantitative Phosphoproteomics Identifies Filaggrin and other Targets of Ionizing Radiation in a Human Skin Model." Experimental Dermatology 21(5):352–357. doi:10.1111/j.1600-0625.2012.01470.x
Yang F, KM Waters, JH Miller, MA Gritsenko, R Zhao, X Du, EA Livesay, SO Purvine, ME Monroe, Y Wang, DG Camp, II, RD Smith, and DL Stenoien. 2010. "Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation." PLoS One 5(11):e14152. doi:10.1371/journal.pone.0014152
Yang F, Y Shen, DG Camp, II, and RD Smith. 2012. "High pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis." Expert Review of Proteomics 9(2):129-134. doi:10.1586/EPR.12.15
Zaborin A, J Defazio, M Kade, BLD Kaiser, N Belogortseva, DG Camp, II, RD Smith, JN Adkins, SM Kim, A Alverdy, D Goldfeld, M Firestone, J Collier, B Jabri, M Tirrell, O Zaborina, and JC Alverdy. 2014. "Phosphate-Containing Polyethylene Glycol Polymers Prevent Lethal Sepsis by Multidrug-Resistant Pathogens." Antimicrobial Agents and Chemotherapy 58(2):966. doi:10.1128/AAC.02183-13
Zhang H, RN Brown, W Qian, ME Monroe, SO Purvine, RJ Moore, MA Gritsenko, L Shi, MF Romine, JK Fredrickson, L Pasa-Tolic, RD Smith, and MS Lipton. 2010. "Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling." Journal of Proteome Research 9(5):2160-2169.
Zhang Q, TL Fillmore, AA Schepmoes, TRW Clauss, MA Gritsenko, PW Mueller, M Rewers, MA Atkinson, RD Smith, and TO Metz. 2013. "Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes." The Journal of Experimental Medicine 210(1):191-203. doi:10.1084/jem.20111843
Zhang X, J Zhou, MH Chin, AA Schepmoes, VA Petyuk, KK Weitz, BO Petritis, ME Monroe, DG Camp, II, SA Wood, WP Melega, DJ Bigelow, DJ Smith, W Qian, and RD Smith. 2010. " Region-Specific Protein Abundance Changes in the Brain of MPTP-induced Parkinson’s Disease Mouse Model ." Journal of Proteome Research 9(3):1496-1509. doi:10.1021/pr901024z
Zhou J, RK Krovvidi, Y Gao, H Gao, BO Petritis, A De, C Miller-Graziano, PE Bankey, VA Petyuk, CD Nicora, TRW Clauss, RJ Moore, T Shi, JN Brown, A Kaushal, W Xiao, RW Davis, RV Maier, RG Tompkins, W Qian, DG Camp, II, and RD Smith. 2013. "Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling." Proteomics - Clinical Applications 7:1-13. doi:10.1002/prca.201200109