Collaborative Research Projects Supported by the NCRR P41 Resource Center
EMSL Project ID
24698
Abstract
The Proteomics Resource Center for Integrative Biology at PNNL was established in 2003 and builds on the unique instrumentation and the infrastructure provided by PNNLs EMSL facility. The mission of the P41 Biomedical Technology Resource Center is to address questions and provide answers to biomedically important research projects that also serve to stimulate the advancement of new technologies developed under the Resource Center. Rapid and comprehensive characterization of proteins and protein modifications and the measurement of absolute protein abundances are extended to a diversity of collaborative projects relevant to human health and the progression of various disease states all of which are revealing new insights into the molecular nature of cell-signaling pathways and networks for the biomedical research community. New proteomic technologies developed during the course of these collaborative research projects will be propagated and disseminated throughout the scientific community.Project Details
Project type
Large-Scale EMSL Research
Start Date
2007-06-06
End Date
2010-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
A Global Survey of ATPase Activity in Plasmodium falciparum Asexual Blood Stages and Gametocytes
Ortega C., A. Frando, B.M. Webb-Robertson, L.N. Anderson, N. Fleck, E.L. Flannery, and M. Fishbaugher, et al. 2018. "A global survey of ATPase activity in Plasmodium falciparum asexual blood stages and gametocytes." Molecular and Cellular Proteomics 17, no. 1:111-120. PNNL-SA-121236. doi:10.1074/mcp.RA117.000088
Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models
Lewis NE, KK Hixson, TM Conrad, JA Lerman, P Charusanti, AD Polpitiya, JN Adkins, G Schramm, SO Purvine, D Lopez-Ferrer, KK Weitz, R Eils, R Konig, RD Smith, and BO Palsson. 2010. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Molecular Systems Biology 6:Article No. 390. doi:10.1038/msb.2010.47
Uterine Deletion of Trp53 Compromises Antioxidant Responses in the Mouse Decidua
Burnum KE, Y Hirota, ES Baker, M Yoshie, YM Ibrahim, ME Monroe, GA Anderson, RD Smith, T Daikoku, and SK Dey. 2012. "Uterine deletion of Trp53 compromises antioxidant responses in mouse decidua." Endocrinology 153(9):4568-4579. doi:10.1210/en.2012-1335
Systems Virology Identifies a Mitochondrial Fatty Acid Oxidation Enzyme, Dodecenoyl Coenzyme A Delta Isomerase, Required for Hepatitis C Virus Replication and Likely Pathogenesis
Rasmussen A, DL Diamond, JE McDermott, X Gao, TO Metz, MM Matzke, V Carter, S Belisle, MJ Korth, KM Waters, RD Smith, and MG Katze. 2011. "Systems Virology Identifies a Mitochondrial Fatty Acid Oxidation Enyzme, Dodecenoyl Coenzyme A Delta Isomerase, Required for Hepatitis C Virus Replication and Likely Pathogenesis." Journal of Virology 85(22):11646-11654. doi:10.1128/JVI.05605-11
Effectiveness of CID, HCD, and ETD with FT MS/MS for Degradomic-Peptidomic Analysis: Comparison of Peptide Identification Methods
Shen Y, N Tolic, F Xie, R Zhao, SO Purvine, AA Schepmoes, RJ Moore, GA Anderson, and RD Smith. 2011. "Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: comparison of peptide identification methods." Journal of Proteome Research 10(9):3929-3943. doi:10.1021/pr200052c
Isotopic Effect on Ion Mobility and Separation of Isotopomers by High-Field Ion Mobility Spectrometry
Shvartsburg AA, DE Clemmer, and RD Smith. 2010. "Isotopic Effect on Ion Mobility and Separation of Isotopomers by High-Field Ion Mobility Spectrometry ." Analytical Chemistry 82(19):8047-8051. doi:10.1021/ac101992d
DtaRefinery, a Software Tool for Elimination of Systematic Errors from Parent Ion Mass Measurements in Tandem Mass Spectra Data Sets
Petyuk VA, AM Mayampurath, ME Monroe, AD Polpitiya, SO Purvine, GA Anderson, DG Camp, II, and RD Smith. 2009. "DtaRefinery: a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra datasets." Molecular & Cellular Proteomics. MCP 9.3:486-496. doi:10.1074/mcp.M900217-MCP200
Blood Peptidome-Degradome Profile of Breast Cancer
Shen Y, N Tolic, T Liu, R Zhao, BO Petritis, MA Gritsenko, DG Camp, II, RJ Moore, SO Purvine, FJ Esteva, and RD Smith. 2010. " Blood Peptidome-Degradome Profile of Breast Cancer." PLoS One 5(10):Article No.: e13133. doi:10.1371/journal.pone.0013133
Pressurized Pepsin Digestion in Proteomics
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
Membrane-Based Emitter for Coupling Microfluidics with Ultrasensitive Nanoelectrospray Ionization-Mass Spectrometry
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
Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells
Wang Y, F Yang, MA Gritsenko, Y Wang, TRW Clauss, T Liu, Y Shen, ME Monroe, D Lopez-Ferrer, T Reno, RJ Moore, RL Klemke, DG Camp, II, and RD Smith. 2011. "Reversed-Phase Chromatography with Multiple Fraction Concatenation Strategy for Proteome Profiling of Human MCF10A Cells." Proteomics 11(10):2019-2026. doi:10.1002/pmic.201000722
Separation of Peptide Isomers with Variant Modified Sites by High-Resolution Differential Ion Mobility Spectrometry
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
Characterization of Macaque Pulmonary Fluid Proteome during Monkeypox Infection
Brown JN, R Estep, D Lopez-Ferrer, HM Brewer, TRW Clauss, NP Manes, M O'Connor, H Li, JN Adkins, S Wong, and RD Smith. 2010. "CHARACTERIZATION OF MACAQUE PULMONARY FLUID PROTEOME DURING MONKEYPOX INFECTION: DYNAMICS OF HOST RESPONSE." Molecular & Cellular Proteomics. MCP 9(12):2760-2771. doi:10.1074/mcp.M110.001875
High-Resolution Differential Ion Mobility Separations Using Planar Analyzers at Elevated Dispersion Fields
Shvartsburg AA, DC Prior, K Tang, and RD Smith. 2010. "High-Resolution Differential Ion Mobility Separations Using Planar Analyzers at Elevated Dispersion Fields." Analytical Chemistry 82(18):7649-7655. doi:10.1021/ac101413k
Combined Pulsed-Q Dissociation and Electron Transfer Dissociation for Identification and Quantification of iTRAQ-Labeled Phosphopeptides
Yang F, S Wu, DL Stenoien, R Zhao, ME Monroe, MA Gritsenko, SO Purvine, AD Polpitiya, N Tolic, Q Zhang, AD Norbeck, DJ Orton, RJ Moore, K Tang, GA Anderson, L Pasa-Tolic, DG Camp, II, and RD Smith. 2009. "Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ–labeled phosphopeptides." Analytical Chemistry 81(10):4137-4143. doi:10.1021/ac802605m
Integrated Workflow for Characterizing Intact Phosphoproteins from Complex Mixtures
Wu S, F Yang, R Zhao, N Tolic, EW Robinson, DG Camp, II, RD Smith, and L Pasa-Tolic. 2009. "An integrated workflow for characterizing intact phosphoproteins from complex mixtures." Analytical Chemistry 81(11):4210-4219. doi:10.1021/ac802487q
Integrated Post-Experiment Monoisotopic Mass Refinement: An Integrated Approach to Accurately Assign Monoisotopic Precursor Masses to Tandem Mass Spectrometric Data
Jung HJ, SO Purvine, H Kim, VA Petyuk, SW Hyung, ME Monroe, DG Mun, KC Kim, JM Park, SJ Kim, N Tolic, GW Slysz, RJ Moore, R Zhao, JN Adkins, GA Anderson, H Lee, DG Camp, II, MH Yu, RD Smith, and SW Lee. 2010. "iPE MMR: An integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data." Analytical Chemistry 82(20):8510-8518. doi:10/1021/ac1013886
Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis Applying Dual-Step 18O Labeling Coupled with Immobilized Metal-Ion Affinity Chromatography
Ding SJ, Y Wang, JM Jacobs, W Qian, F Yang, AV Tolmachev, X Du, W Wang, RJ Moore, ME Monroe, SO Purvine, KM Waters, TH Heibeck, JN Adkins, DG Camp, II, RL Klemke, and RD Smith. 2008. "Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step ¹?O Labeling Coupled with Immobilized Metal-ion Affinity Chromatography." Journal of Proteome Research 7(10):4215-24. doi:10.1021/pr7007785
Novel Ser/Thr Protein Phosphatase 5 (PP5) Regulated Targets during DNA Damage Identified by Proteomics Analysis
Ham BM, H Jayachandran, F Yang, N Jaitly, AD Polpitiya, ME Monroe, L Wang, R Zhao, SO Purvine, EA Livesay, DG Camp, II, SS Rossie, and RD Smith. 2010. "Novel Ser/Thr Protein Phosphatase 5 (PP5) Regulated Targets during DNA Damage Identified by Proteomics Analysis." Journal of Proteome Research 9(2):945-953. doi:10.1021/pr9008207
Enhanced Sensitivity for Selected Reaction Monitoring Mass Spectrometry-based Targeted Proteomics Using a Dual Stage Electrodynamic Ion Funnel Interface
Hossain M, DT Kaleta, EW Robinson, T Liu, R Zhao, JS Page, RT Kelly, RJ Moore, K Tang, DG Camp, II, W Qian, and RD Smith. 2011. "Enhanced Sensitivity for Selected Reaction Monitoring–Mass Spectrometry-based Targeted Proteomics using a Dual-Stage Electrodynamic Ion Funnel Interface ." Molecular & Cellular Proteomics. MCP 10(2):, doi:10.1074/mcp.M000062-MCP201
FT-ICR MS optimization for the analysis of intact proteins
Aleksey V. Tolmachev, ErrolW. Robinson, SiWu, Ljiljana Pa?sa-Toli ´c?, Richard D. Smith. 2008. "FT-ICR MS optimization for the analysis of intact proteins." International Journal of Mass Spectrometry 287 (2009) 32–38. Available online 1 November 2008. doi:10.1016/j.ijms.2008.10.010
Human Cytomegalovirus Secretome Contains Factors That Induce Angiogenesis and Wound Healing
Dumortier J, DN Streblow, AV Moses, JM Jacobs, CN Kreklywich, DG Camp, II, RD Smith, SL Orloff, and J Nelson. 2008. "Human Cytomegalovirus Secretome Contains Factors That Induce Angiogenesis and Wound Healing." Journal of Virology 82(13):6524-6535. doi:doi:10.1128/JVI.00502-08
Characterization of Strategies for Obtaining Confident Identifications in Bottom-Up Proteomics Measurements Using Hybrid FTMS Instruments
Tolmachev AV, ME Monroe, SO Purvine, RJ Moore, N Jaitly, JN Adkins, GA Anderson, and RD Smith. 2008. "Characterization of Strategies for Obtaining Confident Identifications in Bottom-Up Proteomics Measurements Using Hybrid FTMS instruments ." Analytical Chemistry 80(22):8514-8525. doi:10.1021/ac801376g
Fundamentals of Traveling Wave Ion Mobility Spectrometry
Shvartsburg AA, and RD Smith. 2008. " Fundamentals of Traveling Wave Ion Mobility Spectrometry." Analytical Chemistry 80(24):9689-9699. doi:10.1021/ac8016295
Spatial mapping of the neurite and soma proteomes reveals a functional Cdc42/Rac regulatory network
Olivier C. Pertz, Yingchun Wang, Feng Yang, Wei Wang, Laurie J. Gay, Marina A. Gristenko, Therese R. Clauss, David J. Anderson, Tao Liu, Kenneth J. Auberry, David G. Camp II, Richard D. Smith, and Richard L. Klemke. 2007. "Spatial mapping of the neurite and soma proteomes
reveals a functional Cdc42/Rac regulatory network." PNAS 105(6):1931-1936. doi:10.1073/pnas.0706545105
reveals a functional Cdc42/Rac regulatory network." PNAS 105(6):1931-1936. doi:10.1073/pnas.0706545105