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
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
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
Auberry KJ, GR Kiebel, ME Monroe, JN Adkins, GA Anderson, and RD Smith. 2010. "Omics.pnl.gov: A Portal for the Distribution and Sharing of Multi-Disciplinary Pan-Omics Information." Journal of Proteomics and Bioinformatics 3(1):1-4.
A. Umar, H. Kang, A.M. Timmermans, M.P. Look, M.E. Meijer-van Gelder, N. Jaitly, M. Den Bakker, J.W.M. Martens, T.M. Luider, J.A. Foekens, L. Pasa-Tolić. Identification of a putative protein-profile associating with tamoxifen therapy-resistance in breast cancer. Molecular & Cellular Proteomics, 8 (6):1278-1294 (2009)
Baker ES, EA Livesay, DJ Orton, RJ Moore, WF Danielson, DC Prior, YM Ibrahim, BL Lamarche, AM Mayampurath, AA Schepmoes, DF Hopkins, K Tang, RD Smith, and ME Belov. 2010. "An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies." Journal of Proteome Research 9(2):997-1006. doi:10.1021/pr900888b
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
Brown JN, R Palermo, CR Baskin, MA Gritsenko, PJ Sabourin, JP Long, CL Sabourin, H Bielefeldt-Ohmann, A Garcia-Sastre, R Albrecht, TM Tumpey, JM Jacobs, RD Smith, and MG Katze. 2010. "Macaque Proteome Response to Highly Pathogenic Avian Influenza and 1918 Reassortant Influenza Virus Infections." Journal of Virology 84(22):12058-12068.
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
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
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
Gupta N, KK Hixson, DE Culley, RD Smith, and PA Pevzner. 2010. "Analyzing Protease Specificity and Detecting in Vivo Proteolytic Events Using Tandem Mass Spectrometry." Proteomics 10(15):2833-2844.
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
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
Heibeck, T.H.; Ding, S.J.; Opresko, L.K.; Zhao, R.; Schepmoes, A.A.; Yang, F.; Tolmachev, A.V.; Monroe, M.E.; Camp, D.G.; Smith, R.D.; Wiley, H.S. and Qian, W.J. An Extensive Survey of Tyrosine Phosphorylation Revealing New Sites in Human Mammary Epithelial Cells. J. Proteome Res., 2009, 8(8), 3852-61
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
Ibrahim YM, DC Prior, ES Baker, RD Smith, and ME Belov. 2010. "Characterization of an Ion Mobility-Multiplexed Collision Induced Dissociation- Tandem Time-of-Flight Mass Spectrometry Approach." International Journal of Mass Spectrometry 293(1-3):34-44.
Jaitly N, AM Mayampurath, KA Littlefield, JN Adkins, GA Anderson, and RD Smith. 2009. "Decon2LS: An Open-Source Software Package for Automated Processing and Visualization of High Resolution Mass Spectrometry Data." BMC Bioinformatics 10:87.
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. "Integrated Post-Experiment Monoisotopic Mass Refinement: An Integrated Approach to Accurately Assign Monoisotopic Precursor Masses to Tandem Mass Spectrometric Data." Analytical Chemistry 82(20):8510-8518. doi:10.1021/ac101388b
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
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.
Kim J, BC Kim, D Lopez-Ferrer, K Petritis, and RD Smith. 2010. "Nanobiocatalysis for protein digestion in proteomic analysis ." Proteomics 10(4 SP ISS):687-699.
Kotz KT, W Xiao, C Miller-Graziano, W Qian, A Russom, EA Warner, LL Moldawer, A De, PE Bankey, BO Petritis, DG Camp, II, AE Rosenbach, J Goverman, SP Fagan, BH Brownstein, D Irimia, W Xu, J Wilhelmy, M Mindrinos, RD Smith, RW Davis, RG Tompkins, and M Toner. 2010. "Clinical Microfluidics for Neutrophil Genomics and Proteomics." Nature Medicine 16(9):1042-1048. doi:10.1038/nm.2205
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." PNNL-SA-88005, Pacific Northwest National Laboratory, Richland, WA.
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
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
Lopez-Ferrer D, KK Hixson, HS Smallwood, TC Squier, K Petritis, and RD Smith. 2009. "Evaluation of a High Intensity Focused Ultrasound-Immobilized Trypsin Digestion and 18 O-Labeling Method for Quantitative Proteomics." Analytical Chemistry 81(15):6272-6277.
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
Lourette NM, HS Smallwood, S Wu, EW Robinson, TC Squier, RD Smith, and L Pasa-Tolic. 2010. "A Top-Down LC-FTICR MS-Based Strategy for Characterizing Oxidized Calmodulin in Activated Macrophages ." Journal of the American Society for Mass Spectrometry 21(6):930-939.
Marginean I, JS Page, AV Tolmachev, K Tang, and RD Smith. 2010. "Achieving 50% ionization efficiency in sub-ambient pressure ionization with nanoelectrospray." Analytical Chemistry 82(22):9344-9349.
nLC-FTICR in BC
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
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
Petritis, B.O., Qian, W.J., Camp, D.G., and Smith, R.D. A simple procedure for effective quenching of trypsin activity and prevention of 18O-labeling back-exchange. J Proteome Res, 2009, 8, 2157-2163.
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
Petyuk VA, W Qian, RD Smith, and DJ Smith. 2010. "Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry." Methods 50(2):77-84.
Qian, W.J.; Liu, T.; Petyuk, V.A.; Gritsenko, M.A.; Petritis, B.O.; Polpitiya, A.D.; Kaushal, A.; Xiao, W.; Finnerty, C.C.; Jeschke, M.G.; Jaitly, N.; Monroe, M.E.; Moore, R.J.; Moldawer, L.L.; Davis, R.W.; Tompkins, R.G.; Herndon, D.N.; Camp, D.G. and Smith, R.D. Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an (18)O-Labeled "Universal" Reference Sample. J. Proteome Res., 2009, 8, 290-299.
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
Schutzer SE, T Liu, B Natelson, TE Angel, AA Schepmoes, SO Purvine, KK Hixson, MS Lipton, DG Camp, II, PK Coyle, RD Smith, and J Bergquist. 2010. "Establishing the Proteome of Normal Human Cerebrospinal Fluid ." PLoS One 5(6):e10980-. doi:10.1371/journal.pone.0010980
Shah AR, K Agarwal, ES Baker, AM Mayampurath, YM Ibrahim, LJ Kangas, ME Monroe, R Zhao, ME Belov, GA Anderson, and RD Smith. 2010. "Machine learning based prediction for peptide drift times in ion mobility spectrometry ." Bioinformatics 26(13):1601-1607.
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
Shen Y, N Tolic, SO Purvine, and RD Smith. 2010. "Identification of Disulfide Bonds in Protein Proteolytic Degradation Products Using de Novo-Protein Unique Sequence Tags Approach." Journal of Proteome Research 9(8):4053-4060.
Shen Y, N Tolic, SO Purvine, and RD Smith. 2010. "Identification of Disulfide Bonds in Protein Proteolytic Degradation Products Using de Novo-Protein Unique Sequence Tags Approach." Journal of Proteome Research 9(8):4053-4060.
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
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. 2008. " Fundamentals of Traveling Wave Ion Mobility Spectrometry." Analytical Chemistry 80(24):9689-9699. doi:10.1021/ac8016295
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
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
Sigdel, T.K.; Kaushal, A.; Gritsenko, M.A.; Norbeck, A.D.; Qian, W.J.; Xiao, W.; Camp, D.G.II; Smith, R.D.; and Sarwal, M.M. Shotgun Proteomics Identifies Proteins Specific for Acute Renal Transplant Rejection. Proteomics - Clinical Applications 2010, 4(1):1-16
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
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
True LD, H Zhang, M Ye, CY Huang, PS Nelson, PD Von Haller, LW Tjoelker, JS Kim, W Qian, RD Smith, WJ Ellis, ES Liebeskind, and AY Liu. 2010. "CD90/THY1 is over-expressed in prostate cancer-associated fibroblasts and could serve as a cancer biomarker." Modern Pathology 23(10):1346-1356.
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
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
Wu S, NM Lourette, N Tolic, R Zhao, R Robinson, AV Tolmachev, RD Smith, and L Pasa-Tolic. 2009. "An integrated top-down and bottom-up strategy for broadly characterizing protein isoforms and modifications." Journal of Proteome Research 8(3):1347-1357.
Wu S, NM Lourette, N Tolic, R Zhao, R Robinson, AV Tolmachev, RD Smith, and L Pasa-Tolic. 2009. "An integrated top-down and bottom-up strategy for broadly characterizing protein isoforms and modifications." Journal of Proteome Research 8(3):1347-1357.
Xie F, T Liu, W Qian, VA Petyuk, and RD Smith. 2011. "Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics." Journal of Biological Chemistry 286(29):25443-25449.
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
Zhang H., Brown RN., Qian W., Monroe ME, Purvine SO., Moore RJ, Gritsenko MA., Shi L., Romine MF., Fredrickson JK., Pa?a-Tolić L., Smith RD., Lipton MS. Quantitative Analysis of Cell Surface Membrane Proteins Using Membrane-Impermeable Chemical Probe Coupled with 18O Labeling. J. Proteom. Res. 2010, 9, 2160-2169
Zhang X, ME Monroe, B Chen, MH Chin, TH Heibeck, AA Schepmoes, F Yang, BO Petritis, DG Camp, II, JG Pounds, JM Jacobs, DJ Smith, DJ Bigelow, RD Smith, and W Qian. 2010. "Endogenous 3, 4- Dihydroxyphenylalanine and Dopaquinone Modifications on Protein Tyrosine: links to mitochondrially derived oxidative stress via hydroxyl radical." Molecular & Cellular Proteomics. MCP 9(6):1199-1208.
Zhang, X.; Zhou, J.Y.; Chin, M.H.; Schepmoes, A.A.; Petyuk, V.A.; Weitz, K.K.; Petritis, B.O.; Monroe, M.E.; Camp, D.G.; Wood, S.A.; Melega, W.P.; Bigelow, D.J.; Smith, D.J.; Qian, W.J.- and Smith, R.D. Region-specific protein abundance changes in the brain of MPTP-induced Parkinsons disease mouse model. J Proteome Res, 2010, 9, 1496-1509
Zhao R, SJ Ding, Y Shen, DG Camp, II, EA Livesay, HR Udseth, and RD Smith. 2009. "Automated metal-free multiple-column nanoLC for improved phosphopeptide analysis sensitivity and throughput." Journal of Chromatography B 877(8-9):663-670.
Zhou J, AA Schepmoes, X Zhang, RJ Moore, ME Monroe, JH Lee, DG Camp, II, RD Smith, and W Qian. 2010. "Improved LC-MS/MS Spectral Counting Statistics by Recovering Low Scoring Spectra Matched to Confidently Identified Peptide Sequences." Journal of Proteome Research 9(11):5698-5704. doi:10.1021/pr100508p