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Publications

Journal Publications by year


Acknowledgments

All publications that result from utilization of the Resource must acknowledge NCRR grant support. Please include the following acknowledgment statement:

Portions of this research were supported by the NIH National Center for Research Resources (RR18522), and the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory). Pacific Northwest National Laboratory is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RLO-1830.

2008 Journal Publications

Baker ES, KQ Tang, WF Danielson, DC Prior and RD Smith. 2008. "Simultaneous fragmentation of multiple ions using IMS drift time dependent collision energies." Journal of the American Society for Mass Spectrometry 19(3):411-419.
Abstract on PubMed

Belov ME, BH Clowers, DC Prior, WF Danielson, AV Liyu, BO Petritis and RD Smith. 2008. "Dynamically multiplexed ion mobility time-of-flight mass spectrometry." Analytical Chemistry 80(15):5873-5883.
Abstract on PubMed

Callister SJ, LA McCue, JE Turse, ME Monroe, KJ Auberry, RD Smith, JN Adkins and MS Lipton. 2008. "Comparative bacterial proteomics: analysis of the core genome concept." PLoS ONE 3(2):e1542.
Abstract on PubMed

Chin MH, WJ Qian, HX Wang, VA Petyuk, JS Bloom, DM Sforza, G Lacan, DH Liu, AH Khan, RM Cantor, DJ Bigelow, WP Melega, DG Camp, RD Smith and DJ Smith. 2008. "Mitochondrial dysfunction, oxidative stress, and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson's disease." Journal of Proteome Research 7(2):666-677.
Abstract on PubMed

Clowers BH, ME Belov, DC Prior, FD William, Y Ibrahim and RD Smith. 2008. "Pseudorandom sequence modifications for ion mobility orthogonal time-of-flight mass spectrometry." Analytical Chemistry 80(7):2464-2473.
Abstract on PubMed

Clowers BH, YM Ibrahim, DC Prior, WF Danielson, ME Belov and RD Smith. 2008. "Enhanced ion utilization efficiency using an electrodynamic ion funnel trap as an injection mechanism for ion mobility spectrometry." Analytical Chemistry 80(3):612-623.
Abstract on PubMed

Ding SJ, YC Wang, JM Jacobs, WJ Qian, F Yang, AV Tolmachev, XX Du, W Wang, RJ Moore, ME Monroe, SO Purvine, K Waters, TH Heibeck, JN Adkins, DG Camp, RL Klemke and RD Smith. 2008. "Quantitative phosphoproteome analysis of lysophosphatidic acid induced chemotaxis applying dual-step O-18 labeling coupled with immobilized metal-ion affinity chromatography." Journal of Proteome Research 7(10):4215-4224.
Abstract on PubMed

Du XX, F Yang, NP Manes, DL Stenoien, ME Monroe, JN Adkins, DJ States, SO Purvine, DG Camp and RD Smith. 2008. "Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications." Journal of Proteome Research 7(6):2195-2203.
Abstract on PubMed

Ham BM, F Yang, H Jayachandran, N Jaitly, ME Monroe, MA Gritsenko, EA Livesay, R Zhao, SO Purvine, D Orton, JN Adkins, DG Camp, S Rossie and RD Smith. 2008. "The influence of sample preparation and replicate analyses on HeLa cell phosphoproteome coverage." Journal of Proteome Research 7(6):2215-2221.
Abstract on PubMed

Ibrahim YM, ME Belov, AV Liyu and RD Smith. 2008. "Automated gain control ion funnel trap for orthogonal time-offlight mass Spectrometry." Analytical Chemistry 80(14):5367-5376.
Abstract on PubMed

Jacobs JM, KM Waters, LE Kathmann, G David, HS Wiley, RD Smith and BD Thrall. 2008. "The mammary epithelial cell secretome and its regulation by signal transduction pathways." Journal of Proteome Research 7(2):558-569.
Abstract on PubMed

Kelly, RT, JS Page, I Marginean, K Tang, and RD Smith. 2008. “Nanoelectrospray Emitter Arrays Providing Inter-Emitter Electric Field Uniformity.” Anal Chem, 80, 5660-5665.
PMCID: PMC2587423 - Abstract

Kelly RT, JS Page, R Zhao, WJ Qian, HM Mottaz, K Tang and RD Smith. 2008. "Capillary-based multi nanoelectrospray emitters: Improvements in ion transmission efficiency and implementation with capillary reversed-phase LC-ESI-MS." Analytical Chemistry 80(1):143-149.
Abstract on PubMed

Kelly RT, K Tang, D Irimia, M Toner and RD Smith. 2008. "Elastomeric microchip electrospray emitter for stable cone-jet mode operation in the nanoflow regime." Analytical Chemistry 80(10):3824-3831.
Abstract on PubMed

Lopez-Ferrer D, K Petritis, KK Hixson, TH Heibeck, RJ Moore, ME Belov, DG Camp and RD Smith. 2008. "Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: Proteomics on the fly." Journal of Proteome Research 7(8):3276-3281.
Abstract on PubMed

Lopez-Ferrer D, K Petritis, NM Lourette, B Clowers, KK Hixson, T Heibeck, DC Prior, L Pasa-Tolic, DG Camp, ME Belov and RD Smith. 2008. "On-line Digestion System for Protein Characterization and Proteome Analysis." Analytical Chemistry 80(23):8930-8936.
Abstract on PubMed

Lopez-Ferrer D, TH Heibeck, K Petritis, KK Hixson, W Qian, ME Monroe, A Mayampurath, RJ Moore, ME Belov, DG Camp and RD Smith. 2008. "Rapid sample processing for LC-MS-based quantitative proteomics using high intensity focused ultrasound." Journal of Proteome Research 7(9):3860-3867.
Abstract on PubMed

Manes NP, RD Estep, HM Mottaz, RJ Moore, TRW Clauss, ME Monroe, X Du, JN Adkins, SW Wong and RD Smith. 2008. "Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions." Journal of Proteome Research 7(3):960-968.
Abstract on PubMed

Marginean I, RT Kelly, DC Prior, BL LaMarche, KQ Tang and RD Smith. 2008. "Analytical characterization of the electrospray ion source in the nanoflow regime." Analytical Chemistry 80(17):6573-6579.
Abstract on PubMed

Mayampurath AM, N Jaitly, SO Purvine, ME Monroe, KJ Auberry, JN Adkins and RD Smith. 2008. "DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra." Bioinformatics 24(7):1021-1023.
Abstract on PubMed

Metz TO, JS Page, ES Baker, KQ Tang, J Ding, YF Shen and RD Smith. 2008. "High-resolution separations and improved ion production and transmission in metabolomics." Trac-Trends in Analytical Chemistry 27(3):205-214.
Abstract on PubMed

Metz TO, WJ Qian, JM Jacobs, MA Gritsenko, RJ Moore, AD Polpitiya, ME Monroe, G David, PW Mueller and RD Smith. 2008. "Application of proteomics in the discovery of candidate protein biomarkers in a diabetes autoantibody standardization program sample subset." Journal of Proteome Research 7(2):698-707.
Abstract on PubMed

Monroe ME, JL Shaw, DS Daly, JN Adkins and RD Smith. 2008. "MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features." Computational Biology and Chemistry 32(3):215-217.
Abstract on PubMed

Mottaz-Brewer HM, AD Norbeck, JN Adkins, NP Manes, C Ansong, L Shi, Y Rikihisa, T Kikuchi, SW Wong, RD Estep, F Heffron, L Pasa-Tolic and RD Smith. 2008. "Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems." J Biomol Tech 19(5):285-95.
Abstract on PubMed

Page JS, K Tang, RT Kelly and RD Smith. 2008. "Subambient pressure ionization with nanoelectrospray source and interface for improved sensitivity in mass spectrometry." Analytical Chemistry 80(5):1800-1805.
Abstract on PubMed

Pertz OC, Y Wang, F Yang, W Wang, LJ Gay, MA Gristenko, TR Clauss, DJ Anderson, T Liu, KJ Auberry, DG Camp, RD Smith and RL Klemke. 2008. "Spatial mapping of the neurite and soma proteomes reveals a functional Cdc42/Rac regulatory network." Proceedings of the National Academy of Sciences of the United States of America 105(6):1931-1936.
Abstract on PubMed

Petyuk VA, N Jaitly, RJ Moore, J Ding, TO Metz, K Tang, ME Monroe, AV Tolmachev, JN Adkins, ME Belov, AR Dabney, WJ Qian, DG Camp and RD Smith. 2008. "Elimination of systematic mass measurement errors in liquid chromatography-mass spectrometry based proteomics using regression models and a Priori partial knowledge of the sample content." Analytical Chemistry 80(3):693-706.
Abstract on PubMed

Petyuk VA, WJ Qian, C Hinault, MA Gritsenko, M Singhal, ME Monroe, DG Camp, RN Kulkarni and RD Smith. 2008. "Characterization of the mouse pancreatic islet proteome and comparative analysis with other mouse tissues." Journal of Proteome Research 7(8):3114-3126.
Abstract on PubMed

Polpitiya AD, WJ Qian, N Jaitly, VA Petyuk, JN Adkins, DG Camp, GA Anderson and RD Smith. 2008. "DAnTE: a statistical tool for quantitative analysis of -omics data." Bioinformatics 24(13):1556-1558.
Abstract on PubMed

Prichard MN, E Sztul, SL Daily, AL Perry, SL Frederick, RB Gill, CB Hartline, DN Streblow, SA Varnum, RD Smith and ER Kern. 2008. "Human cytomegalovirus UL97 kinase activity is required for the hyperphosphorylation of retinoblastoma protein and inhibits the formation of nuclear aggresomes." Journal of Virology 82(10):5054-5067.
Abstract on PubMed

Qian WJ, DT Kaleta, BO Petritis, HL Jiang, T Liu, X Zhang, HM Mottaz, SM Varnum, DG Camp, L Huang, XM Fang, WW Zhang and RD Smith. 2008. "Enhanced Detection of Low Abundance Human Plasma Proteins Using a Tandem IgY12-SuperMix Immunoaffinity Separation Strategy." Molecular & Cellular Proteomics 7(10):1963-1973.
Abstract on PubMed

Robinson EW, AA Shvartsburg, K Tang and RD Smith. 2008. "Control of ion distortion in field asymmetric waveform ion mobility spectrometry via variation of dispersion field and gas temperature." Analytical Chemistry 80(19):7508-7515.
Abstract on PubMed

Rodland KD, JN Adkins, C Ansong, S Chowdhury, NP Manes, L Shi, H Yoon, RD Smith and F Heffron. 2008. "Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella." Future Microbiology 3(6):625-634.
Abstract on PubMed

Shen YF, KK Hixson, N Tolic, DG Camp, SO Purvine, RJ Moore and RD Smith. 2008. "Mass spectrometry analysis of proteome-wide proteolytic post-translational degradation of proteins." Analytical Chemistry 80(15):5819-5828.
Abstract on PubMed

Shen YF, N Tolic, KK Hixson, SO Purvine, GA Anderson and RD Smith. 2008. "De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins." Analytical Chemistry 80(20):7742-7754.
Abstract on PubMed

Shen YF, N Tolic, KK Hixson, SO Purvine, L Pasa-Tolic, WJ Qian, JN Adkins, RJ Moore and RD Smith. 2008. "Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags." Analytical Chemistry 80(6):1871-1882.
Abstract on PubMed

Shvartsburg AA and RD Smith. 2008. "Fundamentals of Traveling Wave Ion Mobility Spectrometry." Analytical Chemistry 80(24):9689-9699.
Abstract on PubMed

Shvartsburg AA and RD Smith. 2008. "Optimum waveforms for differential ion mobility spectrometry (FAIMS)." Journal of the American Society for Mass Spectrometry 19(9):1286-1295.
Abstract on PubMed

Tolmachev AV, EW Robinson, S Wu, H Kang, NM Lourette, L Pasa-Tolic and RD Smith. 2008. "Trapped-ion cell with improved DC potential harmonicity for FT-ICR MS." Journal of the American Society for Mass Spectrometry 19(4):586-597.
Abstract on PubMed

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.
Abstract on PubMed

Umar, A, M Jaremko, PC Burgers, TM Luider, JA Foekens, and L Paša-Tolić. 2008. "High-Throughput Proteomics of Breast Carcinoma Cells: A Focus on FTICR-MS.” Expert Rev Proteomics, 5(3), 445-455.
Abstract on PubMed

Zhang Q, AA Schepmoes, JWC Brock, S Wu, RJ Moore, SO Purvine, JW Baynes, RD Smith and TO Metz. 2008. "Methods for the Enrichment and Analysis of Glycated Peptides." Analytical Chemistry 80(24):9822-9829.
Abstract on PubMed

Zhang Q, N Tang, AA Schepmoes, LS Phillips, RD Smith and TO Metz. 2008. "Proteomic profiling of nonenzymatically glycated proteins in human plasma and erythrocyte membranes." J Proteome Res 7(5):2025-32.
Abstract on PubMed

Zhang Q, VA Petyuk, AA Schepmoes, DJ Orton, ME Monroe, F Yang, RD Smith and TO Metz. 2008. "Analysis of non-enzymatically glycated peptides: neutral-loss-triggered MS3 versus multi-stage activation tandem mass spectrometry." Rapid Communications in Mass Spectrometry 22(19):3027-3034.
Abstract on PubMed

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